As a freshman at the University of Notre Dame in 2000, LoVecchio assumed the starting quarterback role following an injury to Arnaz Battle and two starts by interim QB Gary Godsey, a converted tight-end. He won his first seven games as a starter, during which the team averaged over 400 yards of total offense and 36 points per game. His stats for the season included 1,118 passing yards, eleven touchdowns and only one interception out of 158 attempts. The team was rewarded with a berth in the Fiesta Bowl against Oregon State.
However, the Beavers dominated the Irish in a 41-9 victory. The following year, LoVecchio struggled, losing his first two games and eventually yielding the starting job to Carlyle Holiday. Head coach Bob Davie was fired at the end of the 2001 season, and when new head coach Tyrone Willingham did not name LoVecchio as the starter in the spring of 2002, the quarterback decided to transfer to Indiana University.
After sitting out the 2002 season per NCAA regulations, LoVecchio started eleven games for the Hoosiers in 2003, completing 155 of 291 passes for 1,778 yards and three touchdowns, including an eight-yard touchdown run in the final seconds of a 17-14 win at Illinois. In 2004, he completed 153 of 271 passes for 1,951 yards and thirteen touchdowns.