If you wish to refund a payment, navigate to the payment record and press the “Refund” button. This will show as a standard button in classic, and a quick action in lightning:
You’ll then see the refund dialog, where you can either choose to refund a specified amount (up to the original amount of the payment).
Note that some payment service providers place restrictions on refunds. If this is the case, you will need to contact your payment service provider and ask them to enable refunds on your account.