You do not have to pay to amend a tax return unless the change you made required an upgrade to a higher paid version of the software. And....if that is the case, you must pay for the upgrade upfront with a credit or debit card. You cannot pay for an amended return by having the fee deducted from the refund. When you get a refund for an amended return the IRS will only mail you a check, so it is not possible to have the fees taken out of the refund.