[2][5][6] Rypien graduated early from Shadle Park as a 4.0 grade point average student, earning valedictorian honors.

On August 23, at the close of fall practice, Ryan Finley was named the Broncos' starting quarterback and Rypien was left to redshirt for his freshman season.

[12][13] Rypien entered the game in the second half,[10][14] burning his redshirt, and led the offense to scores on each of his four possessions, three touchdowns and one field goal.

In addition to earning first-team all-conference, Rypien was also awarded Freshman of the Year honors of the Mountain West.

[20] With the hire of new offensive coordinators, and Ryan Finley returning from a broken ankle, Bryan Harsin stated that there would be an open quarterback competition during spring practices.

[22] On April 12, 2016, after the conclusion of spring practices, Ryan Finley announced he would also be transferring to North Carolina State after he graduated in May.

[31] On December 26, 2016, the day before the bowl matchup between Boise State and Baylor, it was announced that Tommy Stuart would transfer after the end of the season.

[33] Also before the start of the season, Rypien represented the offensive side for Boise State at the Mountain West Football Media Days at the Cosmopolitan in Las Vegas,[34] and was named as one of three team captains by his teammates.

In that game, Rypien shared time with dual-threat quarterback Montell Cozart, a graduate transfer from Kansas.

[44] Also before the start of the season, Rypien represented the offensive side for Boise State at the Mountain West Football Media Days at the Cosmopolitan in Las Vegas.

[48] After the second game of the season, he won Mountain West Offensive Player of the Week when he led the Broncos to a 62–7 victory against the University of Connecticut, going 21 of 28 passing for 362 yards and four touchdowns with zero interceptions while helping Boise State put up 818 total yards of offense and a 625 yardage gap between the two teams, the largest gap since 2000.

[10][49] During his strong start to the season, Rypien surpassed Kellen Moore for most 300-yard passing games in school history with 17, and finished his career with 21.

[50] At the conclusion of the season, his efforts won him the MW Player of the year and he was also named the first-team all-conference quarterback of the Mountain West.

[51] On December 26, Rypien and Boise State matched up to play against Boston College in the First Responder Bowl in Dallas, Texas.

NFL analysts commented that he was "comfortable and experienced playing from under center" and an "accurate passer on all three levels", but noted concerns over his hand size and lack of arm strength.

[62] He was promoted to the active roster on November 1, 2019, to be the backup quarterback to Brandon Allen after starter Joe Flacco suffered a neck injury.

[69] He got his first in-game action on September 27, 2020, when he entered the game against the Tampa Bay Buccaneers in relief of starter Jeff Driskel.

[70] On September 29, 2020, Rypien was named the starter for the Broncos Week 4 matchup against the New York Jets on Thursday Night Football.

[71] In his first NFL start, Rypien led the Broncos to a 37–28 victory over the Jets throwing two touchdowns and for 242 yards and three interceptions.

[72] On November 28, 2020, Rypien was placed on the reserve/COVID-19 list after coming in close contact with Jeff Driskel, who tested positive for the virus.

[80] On October 22, 2022, Rypien was named the starter for Denver's Week 7 matchup against the Jets after Russell Wilson was ruled out with a hamstring injury.

[87] Rypien was waived by the Rams on November 7 after losing to the Green Bay Packers in his season starting debut.

On his mother's side of the family, Rypien is the nephew of Chris Tormey, an assistant to the Ottawa Redblacks of the CFL.