Currently, the refund has to go through your payment provider directly. Please have a look at the guide for your payment provider:
Please make sure to create an additional invoice with a negative amount to offset the original invoice. This way your analytics will be correct.
Alternatively, you can issue credit to your member instead of a refund, which will be applied to their next invoice. You can do this by going to the member's profile, clicking the drop-down menu by Charges/Credits, "Add Charge/Credit," then entering a negative amount in the field provided. See the one-time charge guide for more information.
You will no doubt need to offer one-time charges.