The twin blasts killed three people and injured more than 260.
The FBI has already said it investigated 26-year-old Tamerlan Tsarnaev but had found no evidence of a threat.
The officials, who spoke on condition of anonymity, said the CIA added Tsarnaev to the database after Russian intelligence officials contacted their U.S. counterparts in September 2011 about their concerns over Tsarnaev.
The revelations raised fresh questions over why U.S. authorities did not further investigate Tsarnaev, who died last week from injuries after a shoot-out with police.
His younger brother Dzhokhar, 19, has been charged with terror offenses including the use of a weapon of mass destruction.