Hasselbeck earned the starting quarterback spot in preseason as a redshirt junior and played in all 12 games. During the season, he completed 145 of 260 passes for 1,940 yards and 11 touchdowns and also rushed for 198 yards and three touchdowns. In a 24–23 upset win against Syracuse, he was six for 13 in passing for 161 yards and had 11 rushes for 52 and one touchdown. He accounted for 213 of Boston College's 269 yards and was named winner of the Orrie T. Scarminach Award, given to the Most Valuable Player of the Syracuse game. Hasselbeck was named the Big East Co-Offensive Player of the Week after Boston College's 31–29 upset win over Notre Dame. During the game, he completed 20 of 30 passes for 272 yards, accounted for all four of the teams' touchdowns (three pass, one rush), led the team in rushing with 60 yards, and accounted for 332 of Boston College's 442 yards of offense. On November 26, 1999, he completed the longest touchdown pass in Boston College history, a 97-yarder to Dedrick Dewalt in a 38–14 loss against Virginia Tech. After the regular season, Hasselbeck played in the 1999 Insight.com Bowl against Colorado, to whom Boston College lost 62–28 During the game, he completed 13 of 32 passes for 146 yards and a touchdown and rushed for 25 yards.