The raid took place at the bank's information technology offices in Hato Rey, according to US Attorney Rosa Emilia Rodriguez.
Authorities declined to provide details about the investigation, though Rodriguez said it might be related to a probe into the June 2011 killing of New Jersey bank executive Maurice Spagnoletti.
The 56-year-old was fatally shot as he drove home on one of San Juan's main highways, and authorities said it seemed like a professional attack. He had been an executive vice president at Doral for about six months.
Doral Bank also has been involved in a multimillion-dollar feud with the local government. The bank maintains it is owed a USD 230 million refund in overpaid taxes.
The bank said in a statement that FBI agents collected certain information at the bank and that officials are cooperating with authorities.