BC coach Steve Addazio said after the game that Brown was in the hospital with an "internal injury" but would not provide any more information about his condition.
Brown hit the turf hard on his right (throwing) shoulder after being pressured by Clemson's Christian Wilkins on third-and-9 with 17th-ranked Boston College trailing 3-0 early in the first quarter. The Eagles' redshirt sophomore briefly went to the bench before walking to the locker room. He was ruled out in the second quarter.
Brown has started Boston College's first nine games, throwing for 1,567 yards and 16 touchdowns with five interceptions, and adding 94 rushing yards and a touchdown.
He suffered a torn ACL last November but returned in preseason camp.
"Last year was a devastating injury," Addazio said. "I don't know that we're down that path right now. I don't know that."
EJ Perry replaced Brown on BC's second series. Perry, a sophomore who played for the first time since Sept. 22, was 12-of-21 passing for 98 yards after replacing Brown.