A customer paid an invoice though credit card when received by email. Is there any way to reverse the transaction, reimburse the customer and be reimbursed for the fees?

Hi telescopecomptab,

 

Welcome to the Community. Knowing how to record a refund for a customer is essential to keeping your books balanced. QuickBooks Online is a powerful program that offers different tools to assist you in your business bookkeeping. I'll be glad to point you in right direction on this.

If the transaction you're trying to refund the customer was made using the QuickBooks Payments system, there are few steps to take, and this article  Void or refund customer payments in QuickBooks Online can walk you through it.
 

If you are having difficulty entering the customer's credit card information, I recommend that you contact our customer support team as they can take a closer look to help with this.
 

Schedule a Callback or start a Chat: click (?)Help in the upper right in QuickBooks Online > type and enter "Contact support" into the QB Assistant > click Contact Us > explain your situation > click Let's Talk > choose Get a callback or Start a Chat.
Social Media: Facebook, Twitter, and Instagram. Support hours are from Monday to Friday between 9 a.m. and 8 p.m. ET.

Let me know if you have any questions, I'll be happy to help.