You can refund Stripe payments from under the Payment History section of the Checkout menu.

Once you click refund payment,  you will need to select Stripe as the refund method.  Next, select the Stripe payment to refund back to and then enter the amount that you want to refund.  Last, click the save check-mark in the top-right.    The refund will process just like a payment and will return the money to the client's card. 

The refund will also then be referenceable under the payment history section of the checkout menu.

If you run into any issues or have any questions regarding refunding Stripe payments, please chat in to our support team.