Depending on which provider you choose there could be some fees in addition to the standard fees. The standard fees include the discount rate and the per transaction costs. These ancillary online credit card processing fees are the following:
Application fee – Find out about this ahead of time. It is a one-time charge for processing your application for a merchant account. It is nonrefundable and has to be paid regardless of whether the application is approved or not. Note that some companies do not charge this fee.
Setup fee – This charge can range upwards of a $100 and is the cost associated with setting up the shopping cart to connect with the payment gateway. This involves work both on the shopping cart side and the by the processor. Even virtual credit card readers might have setup fees.
Customer support – Some companies charge extra for customer support. This can come in the form of a monthly fee or a charge based on the number of support tickets raised.
American Express – Not all websites support American Express credit cards. Note that there are higher charges when using these cards. This applies to using Amex cards with credit card machines.
IRS fee – This minimal fee helps ensure that your merchant provider is meeting all guidelines provided by the Internal Revenue Service. This can cost an average of about $2, every month.