To refund a payment, open the Invoice Details page for the invoice that the payment was applied to.

OVERVIEW

Open up the invoice you would like to refund. All payments applied to this invoice will be listed in the Activity section on the top of the invoice (pictured below).
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Find the payment that you would like to refund. On the row for that payment, all the way to the right, click Refund.
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You will be given the option to refund the full amount of the payment, or a partial amount of the payment.

MyCase also has a payment Delete feature. Unlike the refund feature you just learned about, deleting a payment completely removes the payment (and leaves no paper trail). This is useful for erroneous payments, or double payments, that have been applied to an invoice. Learn more: How do I delete a payment made on an invoice?