The bank shared a notice to customers in its mobile app on Wednesday, saying some Zelle transactions made between Jan. 14 and Jan. 17 "may be delayed in occurring and posting to accounts as requested."
Bank of America promised the transfers would be completed as soon as possible and offered an apology.
In response to a request for comment, the bank said the issue impacting Zelle transactions had been fixed and customers should be seeing the money in the next few hours.
The notice to customers came as several angry customers shared their issues with Bank of America's customer assistance Twitter account, with some saying the Zelle transfers had "disappeared" from their accounts, pushing their balances into negative territory.
Zelle confirmed that its transactions "outside of Bank of America are not impacted."
Downdetector, which tracks online outage reports submitted by users, indicated a spike in issues with Bank of America around 9 a.m. Eastern.