After redshirting for his freshman year at Memphis in 2012, Lynch was named the Tigers’ starting quarterback prior to the 2013 season. He started all 12 games, completing 203 of 349 passes for 2,056 yards, nine touchdowns and 10 interceptions. As a sophomore in 2014, Lynch started all 13 games. He completed 259 of 413 attempts for 3,031 yards, 22 touchdowns, and nine interceptions. He also rushed for 321 yards and 13 touchdowns. Lynch was named the MVP of the 2014 Miami Beach Bowl after passing for 306 yards with four passing touchdowns and three rushing touchdowns. As a junior in 2015, Lynch again started all 13 games. He completed 296 of 443 passes (66.8%) for 3,778 yards, 28 touchdowns (all five school records) and four interceptions. In Memphis’ 63–0 victory over SMU, Lynch tied an FBS record with seven passing touchdowns in a half. He finished 9 of 14 for 222 yards, and completed his touchdown throws to seven different receivers. After the season, he decided to forgo his senior year and enter the 2016 NFL Draft. Lynch graduated from Memphis in May 2016 with a B.S.E. in sport and leisure management.

Lynch’s 35 touchdowns responsible for in 2014 and 30 in 2015 are first and second in Memphis history, and his 76 for his career is second all-time. He also ranks first and second for most total offense in a season (4,015 yards in 2015; 3,352 in 2014). He has four of the seven most passing yards in a game, including the school record 447 on October 23, 2015 at Tulsa. He ranks second all-time in career attempts, completions, completion percentage, passing yards, and passing touchdowns.

Lynch was predicted to be selected in the first round of the 2016 NFL Draft by draft analysts and in mock drafts prior to the draft. He was rated the third best quarterback in the 2016 draft by NFLDraftScout.com.

The Denver Broncos selected Lynch in the first round (26th overall) of the 2016 NFL Draft in a pick acquired from the Seattle Seahawks for their first and third round pick. He was the third of 15 quarterbacks taken, behind Jared Goff and Carson Wentz, the #1 and #2 overall picks. On June 9, 2016, the Broncos signed Lynch to a four-year, $9,476,296 contract with a $5,091,852 signing bonus.

On October 2, 2016, Lynch played in his first NFL regular-season game against the Tampa Bay Buccaneers, replacing the injured Trevor Siemian. He finished with 170 passing yards on 14 of 24 attempts and threw his first career touchdown pass to wide receiver Emmanuel Sanders in a 27–7 road win at Raymond James Stadium. In Week 5, Lynch started his first NFL game, completing 23 of 35 passes for 223 yards, one touchdown, and one interception in the 23–16 loss to the Atlanta Falcons. He was sacked six times, a record for a Broncos rookie. In Week 13, Lynch again replaced the injured Siemian against the Jacksonville Jaguars, posting 12 completions on 24 passing attempts for 104 yards in a 20–10 win. Overall, he finished his rookie season with 497 passing yards, two passing touchdowns, and one interception.

Going into mini-camps for the 2018 season, it was announced that Lynch would serve as backup quarterback, behind the newly acquired Case Keenum. Two days after the Broncos preseason opener against the Minnesota Vikings, the team announced that Lynch had been demoted to third-string quarterback as Chad Kelly was promoted to backup. He was released by the Broncos on September 2, 2018, after the team acquired Kevin Hogan. In two seasons with the team, Lynch made just four starts and threw four touchdowns and four interceptions.

On January 17, 2019, Lynch signed with the Seattle Seahawks after spending the 2018 season as a free agent. He was waived on August 30, 2019 during final roster cuts.

On September 17, 2019, Lynch was signed to the Pittsburgh Steelers practice squad. He was promoted to the active roster on October 11, 2019 following an injury to Mason Rudolph.

On September 5, 2020, Lynch was waived by the Steelers during final roster cuts.