What is a good rate for credit card processing for an e-commerce site. The challenging thing in getting an answer on this is so many companies make pricing difficult to understand with things like tiered pricing, random fees, and difficult to follow pricing structures. One approach I recommend is finding a credit card company that is has a flat rate for e-commerce transactions (also called card not present). The best published flat rate I have scene for card not present or online purchase flat rates is from National Discount Merchant Services can be scene at this link. At the current time that rate is 1.99%.