Best HR and Payroll Systems for Mid-Sized Companies in Malaysia

Mid-market companies in Malaysia face a unique set of challenges when it comes to managing their human resources and payroll operations. As your team grows, what worked for a smaller enterprise can quickly become cumbersome, leading to costly errors, compliance risks, and high administrative load.

Choosing the right HR payroll system Malaysia is no longer a matter of mere convenience; it is an essential strategy for accuracy, efficiency, and statutory compliance. This guide will educate HR and finance leaders on the top solutions, position the best option for complex needs, and help you align the right vendor to your buying intent.

Why Mid-Sized Companies Need a Modern HR Payroll System Malaysia

Mid-sized business owners, HR managers, and payroll specialists are often bogged down by complex administrative tasks associated with HR payroll system Malaysia. The shift from a simple spreadsheet to an integrated Human Resources Information System (HRIS) and payroll software is critical to support growth and stability.

The challenges of scaling HR payroll system Malaysia

Growing companies in Malaysia commonly struggle with:

• Manual statutory calculations: Ensuring accurate and timely contributions for EPF, SOCSO, EIS, HRDF, and PCB (Potongan Cukai Bulanan) is highly time-consuming and prone to human error.
• Multi-entity payroll complexity: Managing payroll for different entities or subsidiaries within the country adds layers of administrative difficulty.
• Disconnected HR tools: Using separate, non-integrated tools for different functions (e.g., one for leave, one for payroll) causes significant workflow delays and data discrepancies.
• High admin load: Daily tasks like processing claims, managing attendance, and tracking leave consume too much time that could otherwise be spent on strategic planning.

The essential benefits of integrated HRIS and payroll software

A modern, integrated solution helps solve these challenges by offering:

• Automated statutory compliance: Systems automatically calculate and process contributions for all mandatory Malaysian statutes (EPF/SOCSO/EIS/HRDF, PCB).
• More accurate PCB tax calculations: Automated systems drastically improve the accuracy of monthly tax deductions and annual statutory filings, supporting requirements like LHDN e-filing.
• Audit-ready payroll reports: Centralized data and automated processes provide clear, traceable payroll reports, making internal and external audits simple and stress-free.
• Employee self-service access: Employees can manage their own leave applications, view payslips, and submit claims via mobile or web, significantly reducing the administrative load on HR.
• Centralized data: All HR and payroll data is stored in one system, enabling better decision-making through comprehensive reports and analytics.

Why Omni HR is the Ideal HR Payroll System for Malaysia Companies

If you’re a growing or mid-sized company in Malaysia managing complex payroll requirements, statutory contributions, or planning global expansion, choosing the right HR payroll system Malaysia businesses can rely on is crucial. 

Omni HR is built specifically for Asian companies, with Malaysia statutory compliance built into payroll and HR workflows. As a modern payroll management system Malaysia teams trust, Omni reduces manual work while ensuring accuracy at every step. Here’s what sets Omni apart: 

Automated statutory compliance

Omni automates core Malaysia payroll obligations, including EPF, SOCSO, EIS, and PCB calculations. Our platform supports accurate reporting and readiness for LHDN e-filing, helping teams stay compliant with tax requirements while reducing errors and last-minute corrections.

With real-time updates aligned with regulatory changes, payroll stays accurate without relying on manual tracking or spreadsheets.

"Now we literally run payroll in no more than two hours. Before it was two days." 
— Elena Argyriou, Chief of Staff at Snappymob

Multi-country payroll support for SEA expansion 

For companies operating beyond Malaysia, Omni supports compliant payroll across Singapore, the Philippines, Hong Kong, Indonesia, and other regional markets. With localized tax rules, statutory contributions, and multi-currency payments, Omni enables seamless regional payroll from a single platform.

This makes Omni a scalable HR payroll system Malaysia companies can continue using as they expand across Southeast Asia.

Employee self-service and mobile experience 

Omni’s employee self-service portal and mobile app reduce HR workload by enabling employees to manage routine tasks independently. Payslips, leave applications, claims submissions, and personal information updates are all accessible in one place, improving transparency and employee experience.

Complete HRIS: leave, performance, attendance, recruitment 

Omni is more than a payroll tool. It’s a complete payroll management system Malaysia teams can integrate with daily HR operations. 

See Omni integrations

Manage leave, performance reviews, attendance, employee records, and more in one centralized system, eliminating fragmented tools and manual handoffs.

"Omni's holistic system has allowed us to be more action driven rather than process driven. It's 100% worth the investment, I'm quite confident we can grow across Southeast Asia with Omni." 
— Jack Ang, Head of People at Lucence

Advanced reporting & analytics

Omni provides real-time dashboards covering payroll costs, statutory contributions, headcount, and leave trends. Customizable reports support internal audits, budgeting, and payroll reconciliation, while giving finance and HR leaders clearer visibility into workforce data.

Local support for Malaysian customers 

With dedicated local support, Malaysia-based teams receive timely assistance from specialists who understand local payroll regulations, statutory contributions, and LHDN e-Filing requirements, ensuring issues are resolved quickly and accurately.

"The support from Omni over Slack has been fantastic. Having the team right here in the region means they understand our needs and can respond quickly. It's a completely different experience from raising a ticket and waiting 24-48 hours for a response." 
— Derek Tan, Head of HR at Milieu Insight

Best HR and Payroll Systems for Mid-Sized Companies in Malaysia

1. Omni HR

Omni HR is an all-in-one HR and payroll platform designed for Asia’s fast-growing companies. It combines Malaysia statutory compliance with multi-country payroll capabilities, making it ideal for businesses managing both local and regional workforces.

Key features:

• Automated compliance for EPF, SOCSO, EIS, HRDF, PCB, and readiness for LHDN e-Filing
• Full HRIS modules, including leave, performance, recruitment, claims, and time-off
• Multi-country payroll for regional expansion across Southeast Asia
• Real-time analytics and customizable reporting
• Employee self-service portal and mobile app

Strengths:

• Simplifies Malaysia payroll compliance without manual work
• Replaces multiple HR tools with one unified platform
• Scales easily for regional expansion in Southeast Asia
• Gives leadership real-time visibility into workforce data
• Reduces HR admin through employee self-service
• Backed by responsive, Malaysia-based support

Best for:
Mid-sized companies that need a reliable HR payroll system Malaysia businesses trust for local statutory compliance and scalable multi-country payroll.

Pricing: Starts from $3 per employee per month. Find the perfect pricing plan for your budget.

2. Deel

Deel is a strong HR payroll system Malaysia for companies whose growth strategy involves hiring global or remote talent.

Key features: 

• Global payroll for employees and contractors across multiple countries
• Contractor management with localized contracts and payments
• Comprehensive multi-country compliance support
• Fast, compliant onboarding for international hires

Strengths: 

• Simplifies global hiring and contractor management
• Strong compliance coverage across multiple jurisdictions
• Well-suited for distributed and remote-first teams

Best for: 

Companies hiring international or remote teams in Malaysia and managing global contractors.

‍Pricing: Varied pricing based on modules.

3. BrioHR

BrioHR provides a cloud-based HRIS primarily catering to SMEs looking to digitize core HR processes.

Key features: 

• Core HR modules, including leave, performance, and attendance tracking
• Basic payroll functionality
• Intuitive dashboards and reporting tools
• Cloud-based system for centralized HR management

Strengths: 

• Easy to use and quick to adopt
• Covers essential HR needs in one platform
• Suitable for teams prioritizing simple HR digitization

Best for:

SMEs seeking a complete, cloud-based HRIS platform that includes simple payroll functionality.

Pricing:

Available on vendor website (often tiered based on the number of employees and modules used).

4. PayrollPanda

PayrollPanda specializes in straightforward, compliant HR payroll system Malaysia. 

Key features:

• Automated EPF, SOCSO, and EIS calculations
• Accurate PCB tax calculations
• Payslip generation and basic payroll reporting
• Focused payroll-only functionality

Strengths:

• Simple and reliable payroll processing
• Strong focus on Malaysia statutory compliance
• Minimal setup and low operational complexity

Best for:
Companies looking for a dedicated, Malaysia-compliant payroll solution without needing a full HRIS.

Pricing: 

Available on the vendor website (usually based on a monthly fee per employee).

5. Swingvy

Swingvy focuses on providing a user-friendly and mobile-accessible HR payroll system Malaysia for day-to-day use.

Key features:

• Payroll automation with statutory compliance (EPF, SOCSO, EIS)
• Mobile-enabled leave and claims management
• Employee self-service tools for daily HR tasks
• Focus on ease of use and accessibility

Strengths:

• Strong employee experience and mobile usability
• Easy adoption for day-to-day HR operations
• Suitable for teams prioritizing usability over complexity

Best for:
Companies needing a mobile-enabled HR and payroll system for daily operational management.

Pricing: 

Available on vendor website (typically a tiered monthly subscription).

Comparison Table

How to Choose the Right HR Payroll System Malaysia

Selecting the ideal HR payroll system Malaysia requires aligning your long-term operational needs with the system's capabilities. Use this checklist to evaluate potential vendors:

• Local statutory compliance accuracy: Does the system offer automated and reliable calculations for all local statutes, including EPF, SOCSO, EIS, HRDF, and PCB?
• Multi-country payroll capability: If you plan to scale outside of Malaysia in the next 3-5 years, does the system support multi-country payroll management?
• Required HRIS modules: Do you need a full suite covering leave, performance management, and recruitment, or just basic attendance and payroll?
• Self-service and mobile capabilities: Will the system enable employee self-service and mobile access to cut down on HR administrative tasks?
• Data analytics and reporting: Does the system provide the level of centralized data and analytics you need for better decision-making?
• Budget vs. Operational ROI: Consider the long-term Return on Investment (ROI) from increased efficiency and reduced compliance risk, not just the initial cost. Want to calculate the ROI yourself?‍

Check out Omni’s ROI calculator

Choosing the Best HR Payroll System in Malaysia for Mid-Sized Teams

Mid-sized companies in Malaysia face increasing payroll and compliance challenges, from EPF, SOCSO, EIS, to PCB and multi-entity management. Modern HR payroll management system Malaysia are essential for accuracy, efficiency, and compliance. 

While systems like Deel, BrioHR, PayrollPanda and Swingvy offer strong features, Omni HR delivers the most complete and scalable platform for modern, mid-sized teams, with automated statutory compliance and multi-country payroll built in. Book a demo with our team today and see why Omni is the HR payroll system Malaysia for you. 

Frequently Asked Questions

1. What is an HR payroll system, and why does my mid-sized company need one?

An HR payroll system in Malaysia is a comprehensive software platform that automates payroll processing, employee management, and compliance with local regulations such as EPF, SOCSO, EIS, HRDF, and PCB. Unlike basic payroll tools, it integrates leave management, performance reviews, recruitment, and attendance tracking into a single system.

Mid-sized companies in Malaysia need this because manual payroll and HR processes become unsustainable as teams grow. An automated HR and payroll system eliminates errors, saves time, and ensures statutory compliance.

2. Can Omni HR handle Malaysia payroll tax and multi-country payroll simultaneously?

Yes. Omni HR manages both Malaysia payroll compliance and multi-country payroll operations at the same time.

For Malaysia, the platform automates EPF, SOCSO, EIS, HRDF, and PCB calculations and supports LHDN e-Filing with real-time regulatory updates. For regional expansion, Omni supports compliant payroll across Singapore, the Philippines, Hong Kong, Indonesia, and other countries, with multi-currency payments and localized statutory contributions. This makes it ideal for mid-sized companies scaling across Southeast Asia.

3. How does HRIS and payroll software simplify leave, performance, and recruitment management?

An HRIS and payroll system like Omni HR consolidates all HR functions into a single platform.

• Leave management: Employees submit leave requests via a self-service portal or mobile app. Managers approve with one click, and leave balances update automatically.
• Performance management: Set up customizable review templates, automate appraisal cycles, and track employee progress.
• Recruitment: Omni’s built-in ATS posts jobs to multiple boards, tracks candidates, and streamlines onboarding with e-signatures. All employee data integrates with payroll automatically for seamless setup.

This reduces administrative work and ensures compliance with Malaysia labor regulations.

4. What is the difference between a basic payroll app and a full HR payroll system?

A basic payroll app only handles salary calculations and payslips.

A full HR payroll system Malaysia like Omni HR offers:

• Complete HRIS functionality (recruitment, onboarding, time tracking, performance, leave, document management)
• Advanced compliance automation for EPF, SOCSO, EIS, HRDF, PCB, and LHDN e-Filing
• Multi-country payroll capabilities
• Integrations with accounting and communication tools
• Advanced analytics and real-time reporting
• Scalability for teams of 30–200+ employees

For mid-sized companies, a full system eliminates manual data entry and allows HR teams to focus on strategic initiatives.

5. Is my employee data secure in an HRIS payroll system?

Yes. Modern HRIS payroll systems use enterprise-grade security measures, including AES-256 encryption, ISO 27001-certified data centers, PDPA compliance, role-based access controls, and audit trails.

At Omni HR, all sensitive employee data is protected with these security protocols, ensuring compliance with Malaysia’s PDPA and safeguarding confidential information.

6. Can an HR payroll system integrate with my existing accounting software?

Yes. Modern HR payroll systems integrate seamlessly with popular accounting platforms. These integrations sync payroll data, expense claims, and employee costs automatically, reducing errors and eliminating double data entry.

Omni HR integrates with Xero, Slack, Google Calendar, and other essential business tools, keeping your financial and HR data synchronized without additional cost.