To set up a credit card payment method fee, you need to be on the Growth Plan with Shopify Plus.
In the app admin, click Create Fee. Or click View Fees if you want to edit an existing fee.
If you’re creating a new fee, choose the Function Method.
Under the Payment Methods section, click Add Payment Methods.
Check Credit Cards and/or Paypal.
Click Save.
This will add the fee only when a customer pays by credit card or Paypal.
If you’d like to see a walkthrough, you can watch the quick video below: