Payment gateway fees in Malaysia: A complete guide (2026)

Key Takeaways:

• Payment gateway fees in Malaysia go beyond the Merchant Discount Rate (MDR). You also pay for chargebacks, FX conversion, and potentially setup or annual fees.

• Different payment methods carry very different fee structures: FPX is typically flat-rate per transaction, while card and Buy Now Pay Later (BNPL) fees are percentage-based and can be significantly higher.

• Airwallex charges no monthly fees and offers like-for-like settlement in up to 12 currencies, which removes the gateway-level FX conversion fee that most Malaysian businesses don't realise they're paying.

Payment gateway fees in Malaysia are rarely as simple as the percentage your provider advertises.

Most providers lead with their Merchant Discount Rate (MDR), which is the percentage deducted from each transaction before you receive the funds. However, that’s only one part of what you actually pay.

This guide breaks down every type of payment gateway fee you may encounter in Malaysia, explains how each one works, and shows you how to calculate your actual cost of acceptance.

If you already have a good understanding of how payment gateway fees work and want to compare what different providers charge, head straight to our article on the top payment gateway providers in Malaysia. 

What is a payment gateway fee?

A payment gateway fee is the cost your business pays to accept digital payments — whether by card, bank transfer, e-wallet, or Buy Now Pay Later. Every time a customer completes a transaction, the gateway deducts its fees before the remaining funds reach you.

The most visible component is the MDR, but gateway fees also cover the infrastructure behind the transaction: fraud detection, data encryption, and settlement processing.

For a full explanation of how payment gateways work in Malaysia, see our guide to payment gateways.

Types of payment gateway fees in Malaysia

Payment gateways in Malaysia can charge you in several different ways. Here’s a quick overview, before we go into the details:

The information in this table has been reviewed to be accurate as of 5 June 2026.

1. Transaction fees (MDR)

The Merchant Discount Rate is the most visible payment gateway fee. It is expressed as a percentage of each transaction value and deducted before you receive the funds.

In Malaysia, MDR ranges from around 1% to 3% or more. To illustrate: if a customer pays RM500 and your MDR is 2%, the gateway deducts RM10 and you receive RM490.

2. FPX fees

Financial Process Exchange (FPX) fee structures vary significantly by gateway.

Some providers — particularly local ones — charge a flat fee per FPX transaction, which works out cheaper for lower-value sales.

Global gateways often apply a percentage-plus-fixed model: Stripe, for example, charges 3% + RM1.00 per FPX transaction.²

3. Card fees

Most gateways apply two tiers for card payments: domestic cards and international cards.

International cards attract a surcharge on top of the base MDR. On Stripe, that surcharge is an additional 1% for international cards, plus a further 2% if currency conversion is required.²

3. E-wallet fees

E-wallet MDR is generally lower than card MDR, which makes local wallets a cost-effective option for merchants where customers use them.

Rates vary by wallet and provider. On Stripe, GrabPay is charged at 3% per transaction, and Alipay at 2.9% + RM1.00.² Providers with deeper local acquiring relationships may offer lower rates for Malaysian wallets such as Touch 'n Go and ShopeePay.

4. Buy Now Pay Later (BNPL) fees

BNPL carries the highest MDR of any payment method category, reflecting the credit risk the BNPL provider absorbs on each transaction.

Before activating BNPL, check whether the increase in average order value from your customers justifies the higher cost — the answer varies by product type and transaction size.

5. Setup, annual, and monthly fees

Not every gateway charges these, but some do. Stripe charges no setup fees, monthly fees, or hidden fees.² Traditional and domestic gateways may charge onboarding or annual subscription fees in exchange for lower per-transaction MDR, local support, or additional features.

Factor these in when comparing total cost across providers — a zero-MDR introductory offer can still cost more once recurring fees are included.

6. Chargeback and refund fees

A chargeback fee is charged each time a customer disputes a payment with their bank and the dispute is raised to the gateway.

Stripe charges RM90 per dispute received, and a further RM90 if you choose to counter the dispute by submitting evidence. If you win the counter, the evidence fee is returned; if you lose, it is not.²

6. FX conversion fees at the gateway level

When a customer pays you in a foreign currency and your gateway converts that amount to ringgit before paying you out, it charges an FX conversion fee. Stripe charges an additional 2% when currency conversion is required.²

This is different from the foreign transaction fees that your bank charges when you spend in a foreign currency — for that topic, see our foreign transaction fees guide.

7. SST on gateway fees

In Malaysia, Sales and Services Tax (SST) applies to the gateway's service fee, not to the value of your customer's purchase. As a merchant, you bear this cost as part of your operating expenses.

Not all gateway charges are subject to SST; applicability depends on the nature of the service. Check your gateway statements to confirm whether SST appears as a separate line item or is embedded in the total fee.

How to calculate your total cost of acceptance

Comparing providers on MDR alone is misleading. Your effective rate — the true percentage of revenue you pay in fees — depends on several factors. These include your transaction mix, average order value, monthly volume, and how often customers dispute payments.

Here is how to calculate it. Take a hypothetical Malaysian business processing RM20,000 per month, with an average transaction value of RM200 across 100 card transactions:

• MDR at 2.9%: RM580

• Fixed fee at RM1.50 per transaction: RM150

• One chargeback at RM90: RM90

• Monthly fee: RM0

• Total fees: RM820

• Effective rate: 4.1%

The effective rate of 4.1% is well above the advertised 2.9% MDR, and this is the true rate you should keep in mind.

The table below shows how the effective rate shifts as volume grows:

Figures are illustrative only, based on a hypothetical merchant scenario.

At higher volumes, the fixed-fee component becomes proportionally smaller, which lowers your effective rate. That is why volume-based negotiation — which we cover in the next section — is worth considering once your monthly processing grows.

How to reduce your payment gateway fees

A few deliberate choices can meaningfully lower what you pay in gateway fees each month. Here are a few methods you can use:

1. Optimise your payment method mix

Different payment methods carry different costs.

FPX bank transfers are typically cheaper per transaction than card payments, particularly for higher-value orders. If your checkout currently defaults to card, consider making FPX equally prominent for Malaysian customers.

Shifting even a portion of transactions to a lower-cost rail reduces your blended effective rate.

2. Negotiate once your volume grows

Most gateway pricing is not fixed. Once your monthly processing volume reaches a meaningful threshold, you have grounds to negotiate a lower MDR directly with your provider. Contact your account manager and bring your monthly volume figures when negotiating.

3. Avoid unnecessary FX conversion

If you receive payments from international customers, check whether your gateway converts those payments to ringgit before paying you out. That conversion triggers an additional FX fee on top of your MDR.

Providers that offer like-for-like settlement — paying out in the same currency the customer paid in — let you hold the foreign currency and convert it on your own terms. Airwallex, for example, supports settlement in up to 12 currencies in Malaysia, which removes the gateway-level FX conversion fee entirely.

4. Choose a provider that matches your volume

If your monthly transaction volume is lower, a provider with no setup or monthly fees will cost you less overall, even if the per-transaction MDR is slightly higher. Run the total cost calculation from the previous section before committing.

Why Malaysian businesses choose Airwallex

When it comes to payment gateway fees, the total cost is what matters, not just the headline MDR. Many providers layer on setup fees, monthly fees, and FX conversion charges that quietly add up over time.

Airwallex keeps it simple:

• No setup fees, monthly fees, or annual fees. You only pay for what you process.

• Domestic cards from 1.90% + RM0.50, with local payment methods starting from 1.4% + RM0.50.

• Competitive FX conversion rates that save you up to 80% on FX fees. When you receive payments in foreign currencies, you're not losing margin to inflated conversion markups.

The result is a lower effective rate across the board. Malaysian baby care brand Applecrumby, for example, reduced its payment gateway costs by 0.5% and cut international transfer costs by up to RM100 per transaction after switching to Airwallex.

Frequently asked questions (FAQs)

What is a payment gateway fee in Malaysia?

A payment gateway fee is the cost your business pays each time a customer completes a digital payment. It typically includes a percentage of the transaction value (the MDR), and may also include fixed fees, monthly charges, and other add-ons depending on your provider.

What does MDR stand for?

MDR stands for Merchant Discount Rate. It is the percentage deducted from each transaction by your payment gateway before the funds are paid out to you. It is the most visible component of your total gateway cost, but not the only one.

Do payment gateways in Malaysia charge SST?

SST applies to the gateway's service fee, not to the value of your customer's purchase. It appears as a separate cost on your gateway statement and is borne by you as the merchant.

What is a chargeback fee?

A chargeback fee is charged when a customer disputes a payment with their bank and the dispute is escalated to the gateway. It is a per-incident charge, separate from the transaction MDR.

How can I reduce my payment gateway fees?

The most effective ways are to route more customers toward lower-cost payment methods like FPX, negotiate volume-based rates with your provider, and avoid unnecessary FX conversion fees by choosing a gateway that offers like-for-like settlement. Airwallex supports settlement in up to 12 currencies in Malaysia, which removes the gateway-level FX conversion fee for international payments.

Is the cheapest MDR always the best deal?

Not necessarily. A low MDR can be offset by monthly fees, setup costs, chargeback fees, or FX conversion charges. Always calculate your effective rate — total fees divided by total revenue processed — before comparing providers.

Sources:

1. stripe.com/en-my/pricing

This publication does not constitute legal, tax, or professional advice from Airwallex nor substitute seeking such advice, and makes no express or implied representations / warranties / guarantees regarding content accuracy, completeness, or currency. If you would like to request an update, feel free to contact us at [[email protected]]. Airwallex (Malaysia) Sdn. Bhd., a company incorporated under the laws of Malaysia with company registration number 201801007747 (1269761-X), is regulated as a licensed remittance business under the Money Services Business Act 2011 (Licence number 00743 with an expiry date of 3 August 2028, an E-Money Issuer and a registered merchant acquirer under the Financial Services Act 2013.