Colorado (2023–2024)
Hunter transferred to the University of Colorado Boulder in 2023, following Jackson State head coach Deion Sanders. In his FBS debut, Hunter played 147 total snaps across offense and defense in a 45–42 upset win over TCU. In the win, Hunter had 11 receptions for 119 yards and three tackles with an interception on defense. In week 3, Hunter sustained an injury during Colorado's overtime victory over rival Colorado State, which sidelined him for the next three games. Hunter returned from injury week 7 against Stanford where he hauled in a season high 13 catches for 140 yards and two touchdowns. In week 8, Hunter caught two interceptions against number 23 ranked UCLA. In week 9, Hunter had eight catches for 98 yards and a score against number 16 ranked Oregon State. In week 11, Hunter had four receptions for 82 yards and one touchdown against Washington State. In the season finale, Hunter caught eight passes for 107 yards and a touchdown against Utah. On the season, Hunter hauled in 57 receptions for 721 yards and five touchdowns. On defense, he recorded three interceptions and 30 tackles. He totaled 1,036 snaps including 437 on offense, 568 on defense and 31 on special teams, averaging 115.1 per game. He was named a 2023 Consensus All-American and second-team All-PAC-12. Hunter was also named recipient of the Paul Hornung Award.
To open the 2024 season, Hunter had seven receptions for 132 yards and three touchdowns in the win over North Dakota State. In the September 7 game, Colorado was beaten 28–10 by Nebraska. Hunter significantly impacted the offense with 10 catches for 110 yards, but he faced criticism for his lack of effort on the Cornhuskers' first score of the game. In the September 21 game against Baylor, Hunter made the game-winning forced fumble at the goal line in a 38–31 overtime thriller. After finishing the regular season playing nearly 1,400 scrimmage snaps on offense and defense, 382 more than any other player in the country, Hunter won the Heisman Trophy. He was the Colorado Buffaloes second-ever Heisman winner, the first being Rashaan Salaam in 1994. He was also only the second-ever defensive player from the two-platoon system era to win the award, following Charles Woodson in 1997. In addition, Hunter was the first player in college football history to win both the Chuck Bednarik Award, as the nation's top defensive player, and the Fred Biletnikoff Award, as the nation's best wide receiver.
In April 2025, the University of Colorado retired Hunter’s No. 12 jersey during its spring game.