Bank of America says a "routine systems change" - not a WikiLeaks-related attack - was responsible for issues with its online service on Friday.
The problem hit at around 07.00 Eastern Standard Time and was not fully resolved until after 17.00 EST, affecting an unspecified proportion of BofA's 29 million online banking customers.
For those that could access their accounts the system was running slowly but ATM and POS transactions were not affected. The bank took to Twitter, using its BofA_Help account to communicate with dozens of complaining customers.
Bank of America is understood to be the subject of a future WikiLeaks expose, with tens of thousands of internal documents set to be released early this year.
It has also stopped processing payments for the whistleblowing site, attracting the ire of supporters who have attacked the Web sites of PayPal and MasterCard, among others.
However, Friday's outage had "nothing to do with malware, WikiLeaks or any type of attack," a spokeswoman told the Wall Street Journal.