Detmer was born in San Marcos, Texas. He attended Hobby Middle School, Mount Sacred Heart Middle School, and United Middle School in Laredo, Texas, and Southwest High School in San Antonio, Texas. He earned letters in golf, football, basketball, baseball, and track. As a senior, Detmer won All-American honors in football and was the Texas Player of the Year. He also won All-State honors in baseball and All-District in basketball.
In part attracted by the promise of an alcohol-free lifestyle, Detmer attended Brigham Young University (BYU). He redshirted for the Cougars during the 1987 season, and shared quarterback duties with Sean Covey as a freshman in 1988. Detmer started only one game that year, but he made the most of the opportunity, passing for 333 yards and 5 touchdowns in a 65-0 victory over New Mexico. Later, he was named Most Valuable Player of the 1988 Freedom Bowl, after entering the game as a substitute and leading BYU to a come-from-behind 20–17 victory over Colorado.
Detmer became a full-time starter in 1989. He emerged as one of the top quarterbacks in the nation, passing for 4,560 yards and 32 touchdowns during the regular season. His passer rating of 175.6 led the NCAA, and he finished second to Houston's Andre Ware in total offense. He led BYU to a WAC Championship, the team's first since 1985. Detmer finished the season with a strong performance against Penn State in the 1989 Holiday Bowl, setting NCAA records for most passing yards (576) and most yards of total offense (594) in a single bowl game. He finished 9th in the Heisman Trophy voting.
Detmer's junior season (1990) ranks as one of the greatest seasons for a quarterback in college football history. Detmer passed for 5,188 yards and 41 touchdowns in 12 regular season games, and finished the year with 42 NCAA records (and tied for five others). The highpoint of the season was BYU's 28-21 upset victory over top-ranked Miami (FL); Detmer led the Cougars by passing for 406 yards and 3 touchdowns against the defending national champions. For his efforts, Detmer was awarded the Heisman Trophy, and received many other honors (including the Maxwell Award and the Davey O'Brien Award). He was named consensus All-America by the Associated Press, UPI, Newspaper Enterprise Association, Football Writers, Walter Camp, Football News, Scripps Howard, and the Sporting News. Unfortunately for Detmer and BYU, the season ended in disastrous fashion: the Cougars lost 59-28 in their final regular season game (against Hawaii), then lost 65-14 to Texas A&M in the 1990 Holiday Bowl. Detmer was knocked out of the game against Texas A&M, suffering two separated shoulders that required off-season surgery.
The 1991 season started poorly for BYU. With inexperienced teammates, Detmer could not get BYU's offense going, and the Cougars lost their first three games (road contests against Florida State, UCLA, and Penn State). After a 0–3 start, Detmer and BYU turned things around. The Cougars won eight straight games, and clinched their third consecutive WAC Championship with a spectacular 52–52 tie against San Diego State in their final regular season game. In that contest, BYU fell behind 45–17 before Detmer led a comeback. He finished the game with 599 passing yards and 6 touchdowns, both career highs. In his final game as a Cougar, Detmer passed for 350 yards to lead BYU to a 13–13 tie against heavily-favored Iowa in the 1991 Holiday Bowl. Detmer totaled 4,031 passing yards and 35 touchdowns in regular season play during his senior year. He finished third in the Heisman Trophy voting, but won the Davey O'Brien Award again and also earned the Sammy Baugh Trophy and Today's Top VI Award. Additionally, he was named a consensus All-American.
Detmer finished college with the following career totals: 1,530 pass attempts; 958 completions; 15,031 passing yards; 121 touchdown passes; 14,665 yards of total offense; 135 touchdowns responsible for; and 162.7 passer rating— all NCAA records at the time. In total, he finished his college career with 59 NCAA records and tied for three others. Including statistics from bowl games, Detmer amassed 16,206 passing yards and 127 touchdown passes at BYU. He graduated with a degree in recreation administration.
- Freedom Bowl MVP (1988)
- Heisman Trophy (1990)
Maxwell Award (1990)
Davey O'Brien Award (1990)
UPI Player of the Year (1990)
Sammy Baugh Award (1991)
Davey O'Brien Award (1991)
UPI Back of the Year (1991)
Consensus All-American (1990, 1991)