Interbank transfers, such as paying your credit card, if they are run through the ACH system cost very little (think pennies).
All banks have an account with the fed where they are required to keep a balance of a certain amount (depending on how much they have in deposits, the types of deposits, etc). The earn a earnings credit on that balance that can be used towards the monthly fees assessed by the Fed. The monthly fees come from transactional items (ACH, checks, wires, etc) as well as others. So, the earnings credit can offset the ACH fees, which further drives down the cost.
So, to answer your question...your bank doesn't directly charge Citibank. But, both banks are charged some small fee for processing the transaction through the Fed.
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