Payroll SaaS

Payroll Software in Czech Republic

Czech Payroll Compliance

Our Payroll Platform in the Czech Republic Supports You With

Local Bank Salary Payments
Payroll Reporting & Payslips

Statutory Filings
Custom API Integrations

Dive deeper into Czech Republic

Czech

English

Written by Global Payroll Team

Published on November 6, 2026

Last updated November 6, 2026

Expert Reviewed

Payroll Software in Czech Republic

Mercans Payroll Software is a trusted solution for efficient, compliant, and streamlined payroll management in the Czech Republic. Designed to address the practical needs of Czech payroll, our software helps employers manage payroll processing, Financial Administration (Finanční správa) wage tax reporting, Czech Social Security Administration (ČSSZ) contributions, public health insurance (zdravotní pojištění) contributions, and Czech koruna (CZK) employee payments with confidence.

Mercans Payroll Software is an all-in-one native SaaS solution for complete digitalization of your payroll process. Supporting businesses across more than 160 countries, it is designed for organizations of all sizes, from single entities to global conglomerates. Its scalable architecture and seamless integration across modules enhance the user experience with an intuitive interface that is both simple and effective.

Trusted the world over

Aligned with Czech Payroll Regulations

Finanční správa, ČSSZ & Zdravotní Pojišťovny

Our payroll software for the Czech Republic is designed in alignment with Czech statutory payroll reporting requirements and employer obligations involving authorities such as the Financial Administration of the Czech Republic (Finanční správa České republiky), which administers personal income tax withholding through monthly wage tax advances, the Czech Social Security Administration (Česká správa sociálního zabezpečení, ČSSZ), which administers mandatory pension and sickness insurance contributions under the Labour Code (Zákoník práce), and the public health insurance companies (zdravotní pojišťovny), such as VZP (Všeobecná zdravotní pojišťovna), which administer mandatory health insurance contributions. Built to support the Czech Republic’s monthly reporting to Finanční správa, ČSSZ and the relevant health insurance company, the platform helps businesses manage progressive income tax, social security and health insurance contributions, and Czech koruna (CZK) salary payments with confidence, reducing compliance risk and supporting accurate statutory reporting.

Why Choose Mercans

Native SaaS and payroll platform
Trusted by Fortune Global 500 companies and multinationals
Manage all employment types – employees, freelancers, contractors, expats
More than 100 inbound and outbound integrations are available today
Suitable for enterprise businesses
GDPR aligned, SOC 1 & SOC 2 compliant
Supports multiple currencies
ISO 20000 & ISO 27001 Certified
Global presence and multi-country payroll capabilities
OWASP ASVS aligned

Payroll Software Modules

Mercans Payroll Software offers managers and employees a powerful and intuitive online portal designed to streamline and enhance your HR and payroll activities.

Our advanced software modules are equipped with functionality to support efficiency, compliance, and a superior user experience. Learn about them here:

Manager Self Service

Empowers managers to handle HR tasks, including approvals, performance tracking, and employee management, directly from the platform.

Employee Self Service

Provides employees with direct access to their personal information, payroll details, and other HR resources, enhancing transparency and convenience.

Employee Help Desk

Offers a centralized support system for employees to address payroll and HR-related queries, ensuring quick resolution and improved satisfaction.

Data Exchange

Facilitates seamless integration with other systems and platforms through robust data exchange capabilities, streamlining data management and reducing errors.

eDrive and Workflows

Automates and streamlines HR processes with configurable workflows and document management, improving efficiency and compliance.

Time & Attendance

Tracks employee work hours, attendance, and productivity with precision, integrating seamlessly with payroll calculations.

Leave Management

Manages various types of employee leave, including vacation, sick leave, and other absences, with automated approval workflows and accurate tracking.

Loans & Expenses

Handles employee loans and expense claims, ensuring accurate processing and integration with payroll for seamless financial management.

Features of Payroll Software in Czech Republic

Employment Contracts & the Labour Code

Our payroll software supports the Czech Republic’s employment framework under the Labour Code (Zákoník práce, Act No. 262/2006 Coll.), including the default indefinite-term contract and the exception fixed-term contract, which is limited to a maximum aggregate duration of 3 years (including renewals) and capped at 3 consecutive contracts with the same worker, after which it converts to an indefinite-term contract. It can be configured to reflect a probationary period of up to 4 months for regular employees and up to 8 months for managerial employees (or up to half of the agreed term for fixed-term contracts), helping employers manage payroll in line with each employee’s contract type and length of service.

Czech Koruna & SEPA-Compatible Salary Payments

Mercans Payroll Software for the Czech Republic supports processing salary payments in Czech koruna (CZK) into employees’ local bank accounts. The Czech Republic has not adopted the Euro and remains outside the Eurozone, but as a listed Single Euro Payments Area (SEPA) scheme country, statutory withholdings, employer remittances and any euro-denominated cross-border transfers are processed through standard SEPA credit transfers alongside domestic CZK payments, reflecting local market practice.

You have two options:

Option1

Send generated salary payment details from Mercans Payroll Software to Mercans Gateway. The Financial Gateway will then handle the dispatch of payments to Czech banks, supporting locally compliant processing.

Option2

Prepare and process salary and statutory contribution payments directly through your bank from within Mercans, without the need to download a separate payment file.

Mercans facilitates both options to accommodate your payment processing needs efficiently.

Payroll Reporting

Mercans Payroll Software supports accurate and timely payroll data submission for Czech employer reporting obligations. It supports itemized payslip generation, retroactive adjustments, special pay runs, monthly wage tax advance reporting to the Financial Administration (Finanční správa), monthly social security and health insurance contribution reporting to the Czech Social Security Administration (ČSSZ) and the relevant health insurance company, and the annual income tax reconciliation (roční zúčtování).

Earnings and Deductions Calculation

Earnings: Global Payroll for the Czech Republic allows you to define and manage various types of earnings. This includes base salary components, overtime premiums (statutory minimum of 25% of average earnings, or compensatory time off by agreement), and any additional statutory or contractual allowances.
Deductions: The software also supports the definition and processing of different types of deductions. Regular deductions include progressive personal income tax withholding, the employee’s mandatory social security contribution to ČSSZ, and the employee’s mandatory health insurance contribution, while incidental deductions include salary advances and loans.

Taxes

Tax Calculation for Regular and Non-Regular Payments

The Czech Republic applies a progressive monthly personal income tax to the gross salary of resident employees, covering both regular monthly salary and non-regular payments such as bonuses and allowances in the month they are paid, together with the mandatory social security contribution administered by ČSSZ and the mandatory health insurance contribution administered by the employee’s health insurance company.

Personal Income Tax Thresholds and Rates

Since the 2021 abolition of the “super-gross wage”, Czech personal income tax is calculated directly on gross salary at a rate of 15% up to an annual threshold of 36 times the average monthly wage (CZK 1,762,812 for 2026, equivalent to approximately CZK 146,901 per month), with a 23% rate applying to income above that threshold. Resident employees benefit from a basic personal tax credit (sleva na poplatníka) of CZK 30,840 per year (CZK 2,570 per month).

Social Security Contribution Rates (ČSSZ)

Czech mandatory social security contributions are administered by the Czech Social Security Administration (ČSSZ) and cover pension insurance, sickness insurance and the state employment policy contribution. Employees contribute 7.1% of gross salary (6.5% pension insurance plus 0.6% sickness insurance, which became mandatory for employees from 1 January 2024), while employers contribute 24.8% of gross salary (21.5% pension insurance, 2.1% sickness insurance and 1.2% state employment policy contribution). Contributions apply up to an annual maximum assessment base of CZK 2,234,736 (2025 figure, equal to 48 times the average wage and reviewed annually).

Health Insurance Contribution Rates

Mandatory public health insurance (veřejné zdravotní pojištění) totals 13.5% of gross salary with no assessment ceiling: employers contribute 9% and employees contribute 4.5%, remitted to the employee’s chosen health insurance company, such as VZP (Všeobecná zdravotní pojišťovna), the largest Czech public health insurer.

Minimum Wage & Annual Leave

The Czech Republic’s statutory monthly minimum wage is set at national level and reviewed annually (CZK 22,400 per month, equivalent to CZK 134.40 per hour, from 2026). Employees are entitled to a statutory minimum of 4 weeks of paid annual leave per year under the Labour Code.

Tax & Social Security Reporting Deadlines

Employers must remit withheld monthly wage tax advances to the Financial Administration and the related ČSSZ social security and health insurance contributions by the 20th day of the month following the month worked. The annual income tax reconciliation (roční zúčtování) is due by 20 March of the following year for eligible employees.

Termination Notice & Severance

The statutory minimum notice period under the Labour Code is 2 months, commencing on the first day of the calendar month following delivery of the notice. Employees dismissed for organizational reasons are entitled to statutory severance of 1 average monthly salary for under 1 year of service, 2 average monthly salaries for 1 to 2 years of service, and 3 average monthly salaries for 2 or more years of service, rising to 12 average monthly salaries where termination follows a work-related injury or occupational disease.

Mercans payroll software for the Czech Republic efficiently manages and processes social security obligations. This encompasses

ČSSZ Registration

Registration of employees with the Czech Social Security Administration (ČSSZ) and timely enrollment following each new hire.

Contribution Calculation

Calculation of the employee’s 7.1% social security contribution (6.5% pension plus 0.6% sickness insurance) and the employer’s 24.8% contribution (21.5% pension, 2.1% sickness and 1.2% state employment policy).

Health Insurance Coordination

Coordination of mandatory public health insurance contributions (13.5% of gross salary, split 9% employer and 4.5% employee) with the employee’s chosen Czech health insurance company.

Monthly Reporting

Generation of the monthly social security and health insurance contribution reports required by ČSSZ and the relevant health insurance company.

Reporting

Integration of social security and tax obligations into the Financial Administration, ČSSZ and health insurance company reporting systems.

Mercans payroll software for the Czech Republic provides comprehensive tools for managing various types of employee absences

Annual Leave

Administration of the statutory minimum of 4 weeks of paid annual leave per year under the Labour Code.

Public Holidays

Tracking of the Czech Republic’s state-recognized public holidays throughout the calendar year.

Maternity Leave

Management of the statutory maternity benefit (peněžitá pomoc v mateřství) of 28 weeks (37 weeks for multiple births), paid at 70% of the reduced daily assessment base and funded by ČSSZ.

Paternity Leave

Administration of statutory paternity leave (otcovská) of 14 calendar days, paid at 70% and funded by ČSSZ, to be taken within 6 weeks of the child’s birth.

Parental Leave

Management of parental leave (rodičovská dovolená) until the child reaches 3 years of age, alongside the related state parental allowance (rodičovský příspěvek) administered by the Labour Office of the Czech Republic (Úřad práce ČR).

Overtime Pay Calculation

Our system calculates overtime premiums at the statutory minimum of 25% of average earnings (or compensatory time off by agreement), within the statutory cap of 150 hours per year that an employer may order unilaterally, extendable by mutual agreement up to an average of 8 hours per week.

Bank Integration

Global Payroll for the Czech Republic integrates with Czech banking workflows to support secure and efficient payroll processing by automating CZK payment data and minimizing errors.

Payment Files

The software generates and stores the necessary payment files for Czech banks, covering CZK salary payments, ČSSZ and health insurance contributions, and other deductions and benefits.

Statutory Allowances

Support for the calculation and payment of statutory and collectively agreed allowances, including overtime and other premiums.

Reporting

Generation of the monthly reporting and payment files required for Financial Administration, ČSSZ and health insurance company submissions.

Payroll Workflows

Streamlines payroll processes with automated workflows tailored to the needs of Czech businesses, enhancing efficiency and accuracy.

Social Security & ČSSZ

Mercans payroll software for the Czech Republic efficiently manages and processes social security obligations. This encompasses

ČSSZ Registration

Registration of employees with the Czech Social Security Administration (ČSSZ) and timely enrollment following each new hire.

Contribution Calculation

Health Insurance Coordination

Coordination of mandatory public health insurance contributions (13.5% of gross salary, split 9% employer and 4.5% employee) with the employee’s chosen Czech health insurance company.

Monthly Reporting

Generation of the monthly social security and health insurance contribution reports required by ČSSZ and the relevant health insurance company.

Reporting

Integration of social security and tax obligations into the Financial Administration, ČSSZ and health insurance company reporting systems.

Absence Management

Mercans payroll software for the Czech Republic provides comprehensive tools for managing various types of employee absences

Annual Leave

Administration of the statutory minimum of 4 weeks of paid annual leave per year under the Labour Code.

Public Holidays

Tracking of the Czech Republic’s state-recognized public holidays throughout the calendar year.

Maternity Leave

Management of the statutory maternity benefit (peněžitá pomoc v mateřství) of 28 weeks (37 weeks for multiple births), paid at 70% of the reduced daily assessment base and funded by ČSSZ.

Paternity Leave

Administration of statutory paternity leave (otcovská) of 14 calendar days, paid at 70% and funded by ČSSZ, to be taken within 6 weeks of the child’s birth.

Parental Leave

Overtime, Bank and Payment

Overtime Pay Calculation

Bank Integration

Global Payroll for the Czech Republic integrates with Czech banking workflows to support secure and efficient payroll processing by automating CZK payment data and minimizing errors.

Payment Files

The software generates and stores the necessary payment files for Czech banks, covering CZK salary payments, ČSSZ and health insurance contributions, and other deductions and benefits.

Statutory Allowances

Support for the calculation and payment of statutory and collectively agreed allowances, including overtime and other premiums.

Reporting

Generation of the monthly reporting and payment files required for Financial Administration, ČSSZ and health insurance company submissions.

Payroll Workflows

Streamlines payroll processes with automated workflows tailored to the needs of Czech businesses, enhancing efficiency and accuracy.

Payroll Implementation

Mercans’ standard payroll implementation process for the Czech Republic is designed to ensure a smooth transition to our payroll system. This process is customized to meet the specific needs of each client, with timelines and deliverables varying based on complexity, data availability, and the number of parallel runs required. Below is an overview of the key steps involved in our implementation process.

Implementation Planning

Assign resources and define roles for the project. Conduct a kick-off meeting to outline objectives and confirm scope. Develop a detailed implementation calendar and plan. Provide a welcome package with project details and contacts. Schedule weekly update calls or emails to monitor progress. Obtain sign-off on the project scope.

Requirements Gathering

Hold workshops to understand client needs and document them. Complete business blueprinting to detail requirements and perform a gap analysis. Define and document any customization needs, including applicable pay scales and allowance structures. Obtain sign-off on requirements to ensure they meet client expectations. Establish a comprehensive list of payroll-specific requirements.

System Configuration

Set up configurations tailored to Czech payroll requirements. Customize the wage type catalog for relevant pay components, including statutory and collectively agreed allowances. Configure data dictionaries and necessary interfaces for Finanční správa, ČSSZ and health insurance data integration. Adapt reports to meet Czech regulatory standards. Set up Employee Self-Service (ESS) and Manager Self-Service (MSS) features.

Data Migration

Migrate employee and payroll master data and confirm its accuracy. Obtain sign-off on the migrated data to ensure correctness. Verify data integrity and completeness before proceeding with further steps.

Test Payroll Run

Run simulation payrolls to validate system configurations and perform parallel runs with existing systems. Complete test run sign-offs to confirm accuracy and execute end-to-end testing. Conduct user acceptance testing (UAT) and address any issues found.

Payroll Management Transition & Sign-off

Develop a transition plan for moving to live payroll and provide training for users. Implement a hypercare plan for post-go-live support and an escalation plan for critical issues. Create a fallback plan for potential disruptions and complete a go-live checklist for final sign-off.

Payroll Integration

Mercans Global stands out with its extensive reach and robust integration capabilities. Operating across more than 160 countries, Mercans supports connections with payroll, tax, HR, finance, banking, and compliance ecosystems to help employers maintain efficient payroll operations in the Czech Republic.

Recognised Trust Sources

Finanční správa, ČSSZ & Zdravotní Pojišťovny

Mercans’ integration capabilities are designed to support Czech payroll reporting processes and secure data exchange with connected systems, reflecting our commitment to global standards and best practices.

Integration with HCM/ HRMS/ Workforce management platforms

Mercans’ Payroll Software integrates seamlessly with most HCM and payroll software, creating a unified experience between HR administration and payroll processing. Through the Employee Self Service (ESS) feature, employees can directly handle their payroll tasks, such as submitting worked hours or declarations. Once approved, these entries are processed within the payroll system. This efficient integration reduces errors and enhances productivity for both employees and HR administrators.

Custom API Integrations

Mercans provides custom API integrations across diverse industries, including hospitality, catering, theme parks, transport, sports, construction, healthcare, events, promotional sectors, greenhouse horticulture, and fresh produce.

Xero Integration

Integrate Mercans payroll with Xero to sync data, automate HR tasks, and streamline processes. Save time, reduce errors, and focus more on growing your business.

Payroll Reports – Standard, Statutory and Year-End Reports

Mercans’ payroll software is equipped to generate a comprehensive range of reports to support both standard and statutory requirements. These reports provide transparency, accuracy, and ease of integration with financial and regulatory systems.

Mercans Standard Reports

Report	Description
Gross to Net Report	Details employee earnings, taxable wages, employee deductions, employer costs and net pay for each payroll run in the Czech Republic.
Payslip	Generates individual itemized payslips showing gross pay, allowances, deductions, ČSSZ and health insurance contributions, and net pay.
Payroll Register	Provides the employee payroll register used to support Czech payroll administration and ČSSZ/health insurance contribution calculations.
ČSSZ & Health Insurance Contribution Report	Produces the per-employee social security and health insurance contribution data required for monthly filing with ČSSZ and the relevant health insurance company.
Annual Payroll Summary	Generates the annual payroll summary for each employee, summarizing total compensation, statutory deductions and other year-end totals.
Bank Payment File (CZK)	Creates a Czech koruna salary payment file according to client or bank specifications for payroll disbursement.

Statutory Standard Reports

Report	Frequency	Description
Monthly Social Security & Health Insurance Report	Monthly (by the 20th of the following month)	Statutory monthly filing and payment of employee and employer social security contributions to ČSSZ and health insurance contributions to the relevant health insurance company.
Payroll Tax Advance Report	Monthly (by the 20th of the following month)	Statutory monthly filing and remittance of withheld personal income tax advances to the Financial Administration (Finanční správa).
Annual Income Tax Reconciliation (Roční zúčtování)	Annually (by 20 March)	Supports the Financial Administration’s annual reconciliation of personal income tax for eligible employees who do not file a separate tax return.

Year-End Reports

Report	Frequency	Description
Annual Payroll Summary	Annually	Annual employee statement summarizing total compensation, statutory deductions and other required year-end payroll totals.

These detailed reports are designed to support statutory and regulatory requirements, helping ensure efficient payroll management and accurate compliance.

Benefits of Payroll Software

Mercans offers a powerful payroll solution that optimizes payroll administration and HR processes. Here’s how our software benefits your organization:

Streamlined Payroll Processing
Additional Key Features

No External Dependency

Manage payroll directly through our application, eliminating the need for third-party processors.

Integrated HR and Leave Management

Handle payroll, HR tasks, and employee leave requests within one platform, simplifying administrative duties.

Reduced Manual Work

Automate routine tasks to minimize errors and ensure accurate payroll processing.

Customization

Personalize workflows to meet your specific business needs, enhancing efficiency.

Time Savings

Redirect time saved from automation to more strategic activities.

Seamless Integrations

Connect effortlessly with systems and leading HR platforms like SAP Success Factors, Workday, and Oracle for a unified workflow.

Centralized Data Management

Consolidate employee data in one place for easy access, updates, and analysis.

Employee Access

Empower employees with 24/7 access to their personal files.

Mercans’ payroll software provides a comprehensive, secure, and user-friendly solution, streamlining payroll processes and allowing you to focus on your most valuable asset, your people.

24/7 Access

Access payroll data anytime and from any location.

Transparent Pricing

Benefit from a fixed monthly fee plus a per-employee charge with no hidden costs.

Dedicated Support

Get expert assistance and advice to maximize the software’s benefits.

Secure Data Management

Support data protection and integrity with secure online processing and controlled backup practices.

Compliance Assurance

Stay compliant with current fiscal and employment regulations through maintained payroll rules and updates.

Mercans’ payroll software provides a comprehensive, secure, and user-friendly solution, streamlining payroll processes and allowing you to focus on your most valuable asset, your people.

Streamlined Payroll Processing

No External Dependency

Manage payroll directly through our application, eliminating the need for third-party processors.

Integrated HR and Leave Management

Handle payroll, HR tasks, and employee leave requests within one platform, simplifying administrative duties.

Reduced Manual Work

Automate routine tasks to minimize errors and ensure accurate payroll processing.

Customization

Personalize workflows to meet your specific business needs, enhancing efficiency.

Time Savings

Redirect time saved from automation to more strategic activities.

Seamless Integrations

Connect effortlessly with systems and leading HR platforms like SAP Success Factors, Workday, and Oracle for a unified workflow.

Centralized Data Management

Consolidate employee data in one place for easy access, updates, and analysis.

Employee Access

Empower employees with 24/7 access to their personal files.

Additional Key Features

24/7 Access

Access payroll data anytime and from any location.

Transparent Pricing

Benefit from a fixed monthly fee plus a per-employee charge with no hidden costs.

Dedicated Support

Get expert assistance and advice to maximize the software’s benefits.

Secure Data Management

Support data protection and integrity with secure online processing and controlled backup practices.

Compliance Assurance

Stay compliant with current fiscal and employment regulations through maintained payroll rules and updates.

This content was prepared for informational purposes only. As local laws & regulations keep on changing, please consult your tax & legal advisors.

Request a demo

Our team will guide you through our powerful payroll solutions and show you how we can tailor our services to fit your needs.

Please leave this field empty.

FAQs

What payroll functions should a SaaS platform support in the Czech Republic (e.g., gross-to-net salary calculation, payslip generation, Finanční správa, ČSSZ and health insurance withholding, and monthly reporting)?

Mercans payroll software for the Czech Republic delivers end-to-end payroll processing including automated gross-to-net salary calculation, itemized payslip generation, progressive personal income tax withholding, Czech Social Security Administration (ČSSZ) contribution calculation, public health insurance contribution calculation, and the monthly reporting required by the Financial Administration (Finanční správa), ČSSZ and the relevant health insurance company, supporting Czech koruna (CZK) salary payments.

How do payroll SaaS solutions ensure compliance with Czech authorities (Finanční správa, ČSSZ, health insurance companies) and statutory reporting obligations?

Mercans supports compliance by keeping pace with the Czech Republic’s monthly wage tax advance reporting to the Financial Administration and monthly social security and health insurance contribution reporting to ČSSZ and the relevant health insurance company, with accurate remittance deadlines (the 20th of the following month) that reduce the risk of late filings and statutory penalties.

What employer registration and employee data are required (e.g. ČSSZ and health insurance registration, work permits for foreign staff) and how does payroll software assist with this?

Mercans automates onboarding by securely capturing and managing employer and employee data, including Czech Social Security Administration (ČSSZ) registration, health insurance company registration, work and residence permit data for non-EU/EEA foreign nationals, and the mandatory employment contract particulars required under the Labour Code (Zákoník práce), helping employers remain compliant from the first day of employment.

How does payroll software handle Czech Republic-specific components like progressive income tax, social security and health insurance contributions, and CZK salary payments?

Mercans payroll software automatically calculates the Czech Republic’s progressive monthly personal income tax on gross salary (15% up to the statutory threshold and 23% above it), the employee’s 7.1% social security contribution to ČSSZ, the employee’s 4.5% health insurance contribution, and the corresponding employer contributions, while supporting salary payments in Czech koruna (CZK).

Can payroll SaaS integrate with Czech HR and ERP systems and support outsourcing or Employer of Record models?

Mercans offers robust integration capabilities with leading HR and ERP systems, supporting seamless payroll, HR management, and outsourcing models including Employer of Record, for full compliance and efficient management of your Czech workforce.