The short answer
If you only take card payments and your orders are mostly small, iKhokha and Yoco cost the least. If you want the widest choice of payment methods at checkout, PayFast still wins on coverage, but you pay for it on every card transaction. Paystack sits in the middle on price and is the strongest choice if you sell subscriptions or want fast, predictable payouts.
That's the summary. The detail matters more, because the cheapest gateway for a R150 order is not always the cheapest for a R1,500 order - and a few of the differences have nothing to do with fees at all.
We use all four of these. We set up iKhokha, PayFast and Yoco on client shops every month, and we use Paystack for our own subscription products. This comparison comes from building with them, not from an affiliate table.
All fees below are the standard published online rates as at October 2026, excluding VAT. Higher-volume businesses can negotiate lower rates with every provider here, so treat these as the starting point, not the ceiling.
The fees, side by side
Local credit and debit cards (online):
- PayFast: 3.2% + R2.00 per transaction
- Yoco: 2.55% - 2.95%, no fixed fee
- iKhokha: 2.85%, no fixed fee
- Paystack: 2.9% + R1.00 per transaction
Instant EFT:
- PayFast: 2%, with a R2.00 minimum
- Yoco: not offered online - cards and mobile wallets only
- iKhokha: 2%
- Paystack: 2%
Foreign cards:
- PayFast: check their fee page - rates vary by card type
- Yoco: check your agreement - international and Amex rates differ from the headline rate
- iKhokha: 3.25%
- Paystack: 3.1% + R1.00
Monthly and setup fees: none of the four charge a monthly fee or a setup fee for online payments.
Why the fixed fee matters more than the percentage
Most comparisons stop at the percentage. That's a mistake, because two of these gateways add a fixed rand amount to every transaction, and on small orders that fixed amount does more damage than the percentage.
Here's what each gateway charges on a single card payment, using Yoco's standard 2.95% rate:
A R150 order (a takeaway, a coffee subscription, a small gift):
- iKhokha: R4.28
- Yoco: R4.43
- Paystack: R5.35
- PayFast: R6.80
A R500 order (a typical small-shop basket):
- iKhokha: R14.25
- Yoco: R14.75
- Paystack: R15.50
- PayFast: R18.00
A R1,500 order (a larger basket, a service deposit):
- iKhokha: R42.75
- Yoco: R44.25
- Paystack: R44.50
- PayFast: R50.00
On a R150 order, PayFast costs about 60% more than iKhokha. On a R1,500 order, the gap shrinks to around 17%. Paystack and Yoco are almost identical on large orders, but Paystack's R1 fixed fee puts it noticeably behind on small ones.
Over a month, the differences add up. A shop doing 200 card orders at an average of R400 would pay roughly:
- iKhokha: R2,280
- Yoco: R2,360
- Paystack: R2,520
- PayFast: R2,960
That's about R680 a month - R8,000 a year - between the cheapest and most expensive option, before VAT. For a small shop, that's real money.
What changes the picture: EFT
Card fees are only half the story. A growing share of South African shoppers prefer paying straight from their bank account, and Instant EFT is cheaper to accept than cards.
PayFast, iKhokha and Paystack all offer Instant EFT at 2%. Yoco does not offer it online at all.
On a R500 order, EFT costs R10 with any of the three that support it, against R14 to R18 for a card payment. If a meaningful share of your customers would rather pay by EFT - common for higher-value orders and for customers wary of entering card details - a gateway without it leaves money and conversions on the table.
PayFast: the widest checkout, the highest card fees
PayFast has been the default South African gateway for years, and its strength is still coverage. Alongside cards and Instant EFT, it supports Capitec Pay, Apple Pay, Samsung Pay, Google Pay, SnapScan, Zapper, Mobicred, and buy-now-pay-later options like MoreTyme and Payflex.
Choose PayFast when:
- Your customers expect a wide range of payment options at checkout
- You want buy-now-pay-later available without a separate integration
- You need recurring billing and want a mature, well-documented setup
Watch out for: the R2.00 fixed fee on every card payment. It's the most expensive card option here, and noticeably so on small orders. Some of the alternative payment methods carry higher rates than cards, so check the fee for each method you switch on.
Yoco: best if you already use their card machines
Yoco's online gateway is clean, quick to set up, and charges no fixed fee. Its real advantage is unification: if you already use a Yoco card machine in-store, your online and in-person sales sit in one dashboard, settle together, and count towards the same volume-based rate.
Choose Yoco when:
- You already use Yoco card machines and want one provider for everything
- Your customers pay by card, Apple Pay or Google Pay
- You want free standard payouts and a simple setup
Watch out for: no Instant EFT online. If you want to offer EFT, you'll need a second gateway alongside Yoco.
iKhokha: lowest card fees, EFT included
iKhokha is the quiet winner on price. At 2.85% with no fixed fee, it's the cheapest card option for most order sizes, and unlike Yoco it includes Instant EFT at 2%. Refunds carry no extra fee, and support is local and reachable.
Choose iKhokha when:
- Margins are tight and you want the lowest card fees
- You want cards and Instant EFT from one provider
- You run a WooCommerce, Wix or Shopstar shop and want a straightforward plugin
Watch out for: a narrower range of alternative payment methods than PayFast. If you specifically need buy-now-pay-later at checkout, you'll need to add it separately.
Paystack: built for developers and subscriptions
Paystack is newer to South Africa than the others, but it's one of the biggest payment companies in Africa and now part of Stripe. It charges 2.9% + R1.00 on local cards, 2% on EFT, and pays out the next business day, with a R3 fee per payout.
Where Paystack stands apart is the technical side. The API and documentation are excellent, subscriptions and recurring billing are first-class, and it handles things like split payments and passing fees to customers cleanly. That's why we chose it for our own software products.
Choose Paystack when:
- You sell subscriptions, memberships or recurring services
- You're building a custom platform rather than a standard online shop
- Predictable next-day payouts matter for your cash flow
Watch out for: the R1.00 fixed fee makes it slightly more expensive than iKhokha and Yoco on small orders, and the R3 payout fee adds up if you take daily payouts on low volume.
How to decide
You run a small shop and mostly take card payments: iKhokha. Lowest fees, EFT included.
You already use Yoco in-store: Yoco online, and consider adding an EFT option alongside it.
Your customers want every possible way to pay, including buy-now-pay-later: PayFast, and accept the higher card fee as the cost of coverage.
You sell subscriptions or run a custom platform: Paystack.
Your orders are small and frequent: avoid fixed fees where you can. On a R100 order, a R2 fixed fee alone is 2% of the sale.
You don't have to pick just one
Plenty of shops run two gateways - a low-cost card gateway as the default, plus a second for EFT or extra payment methods. On WooCommerce, adding a second gateway is straightforward, and your customers simply see more options at checkout.
For a broader look at the South African payment landscape, including SnapScan, Zapper and Ozow, see our guide to choosing a payment gateway.
Need this set up properly?
Choosing the gateway is the easy part. Getting it integrated, tested, and matched to how your customers actually pay is where most DIY shops go wrong.
If you already have a website and want to start selling, we can add a WooCommerce shop to your existing site from R7,500, with your choice of gateway set up and tested. If you're starting from scratch, see our online shop packages. Either way, book a free 20-minute call and we'll help you pick the right combination for what you sell.