The redshirt freshman, who had helped spark BC's three-game winning streak that was snapped Saturday, crumpled to the ground in pain after making a cut deep in Wolfpack territory without being hit early in the second quarter. His right knee appeared to buckle on the cut.
"It didn't look good," BC coach Steve Addazio said after the 17-14 loss. "What does that mean? I don't know. I don't know what that means.
"Obviously he's going to have to have some testing done, and we're going to have to find out exactly what we're dealing with."
Brown was on the ground for a while before being helped off without putting any weight on the leg. After being examined on the sideline, he left on crutches.
Brown, who won the starting job over graduate Darius Wade during preseason camp, has thrown for more than 1,300 yards with 11 TDs and rushed for another score. Brown was 2-of-5 for 29 yards with an interception before the injury and ran three times for 28 yards.
Wade entered the game after Brown was injured and the offense sputtered.
Wade, a graduate student, completed 8 of 15 passes for 82 yards and was sacked five times.
Coming into the game, BC's offense had averaged 465 yards a game during the winning streak. It was held to 347 on Saturday.