To refund a donation (for both one-time and recurring) made by Stripe, head over to your Donations Page and locate the donation that you want to refund. Click on the Transaction ID (or the blue eye to the very right), and you'll see the refund button on the right hand panel.
When you refund a donation, the donor will receive the entire amount that they donated. The Stripe fees that were already charged will show as a negative amount on your Stripe account. A refund will take approximately 5-10 business days to reflect in the donor's account, and the donation will also be removed from the donation total.
Please note: to refund a donation made via PayPal, an organization will have to log in to their PayPal account and complete the refund from their PayPal dashboard.