As an optionquarterback at Colorado from 1988 to 1991, Hagan produced impressive offensive statistics operating Coach Bill McCartney's "I-Bone" offense. Due to veteran quarterback Sal Aunese being stricken with cancer, he took over the starting duties as a sophomore. When Aunese died, Hagan and the rest of the Buffaloes dedicated their season to their fallen comrade. In that 1989 season, he burst on the college football scene, and became the sixth player in the history of NCAADivision I-A to gain more than 1,000 yards passing and more than 1,000 yards rushing in the same season. He was the starting quarterback in 1990 when Colorado won the NCAA Division I-A national football championship, and in 1989 to 1991 when Colorado was the Big Eight Conference champions. His record as quarterback for Colorado was 28–5–2 (20–0–1 in Big Eight). In Heisman Trophy voting he was 5th in 1989 with 242 points, 17th in 1990 with 17 points and 20th in 1991 with 12 points.
Hagan was inducted into the University of Colorado Athletic Hall of Fame in 2002. He is also considered by many alumni as the best football player in CU history. Hagan went 28-5-2 as a starter for the Buffs, including 20-0-1 in Big Eight Conference play. He finished his career with 3,801 passing yards and 2,007 rushing yards.
Before his last season, he graduated from Colorado with a bachelor's degree in sociology. When his professional football career ended, Hagan turned to jobs in marketing and then in coaching. He became the defensive technical intern in 2004 for Colorado. The following year, he was hired by Gary Barnett as an offensive assistant coach. In 2006, he was one of only two assistant coaches kept by new head coach Dan Hawkins as the running backs assistant coach where he remains today.