If you're linking this fee with a sales receipt or invoice payment, you can create a bank deposit and put the Merchant fee under Add funds to this deposit section by putting a negative sign before the amount. Doing this will offset the total amount of the bank deposit and be able to match it with a bank deposit transaction.
You can follow the steps below:
Sign in to your QuickBooks Online account.
Click on the + New menu at the top and select the Bank Deposit.
Choose a bank account in the Account field.
Check the Sales receipt/Payment box.
Go to the Add funds to this deposit section.
In the Account column, enter Credit Card transaction fees.
Enter the amount as a negative.
Hit on Save and close.
Otherwise, you can create an expense if this merchant fee is a separate expense BANKCARD 8710 MTOT DISC transaction.
Click on the + New menu at the top and select the Bank Deposit.
Choose a bank account in the Account field.
Under Category details, select an expense account.