A bank spokeswoman said Wednesday that the glitch involved about 1,000 transactions and that all duplicate charges will be refunded.
Some customers who used Apple Pay with debit cards issued by Bank of America have complained they were charged twice for a single transaction.
(Also see: Apple Pay Review)
Apple says it was aware of the glitch, which it said affected "a very small number of Apple Pay users." The Cupertino, California-based company has not disclosed how many customers have used Apple Pay since it became available Monday.
(Also see: Apple Pay: Everything You Need to Know)