You can issue refunds through your Payment Processor account. Log in to your WePay, Stripe, etc. account and you will be able to issue refunds there. Be sure to change the status of the User on your Manage List after you do!
For WePay: If a transaction is from over 60 days, you need to email WePay asking for a manual refund. If the transaction is from over 180 days, a refund cannot be issued.
Keep in mind, some of the fees charged for the transaction can not be refunded.