A late bloomer, Allen received no interest from FBS programs after his high school career. He signed with Reedley Community College in California for the 2014 season, throwing for 26 touchdowns and 285 yards a game (with 66 rushing yards per contest) in his lone season there. Wyoming head coach Craig Bohl saw Allen's talent, wondering if he could be another Carson Wentz, the number two overall pick for the Philadelphia Eagles who he recruited and coached at North Dakota State before moving to Laramie. Allen only got a chance to play in two games (4-of-6, 51 yards passing; 3 rushes, 40 yards) for the Cowboys in 2015, starting once, before breaking his right clavicle and taking a medical redshirt. His sophomore season, on the other hand, was healthy and productive. The Cowboys made the Mountain West Conference Championship game with his leadership in 14 starts, completing 56 percent of his passes (209-of-373) throwing for 3,203 yards and 28 touchdowns. That completion percentage and his 15 interceptions showed that his game needs to be tamed, and those concerns were only exacerbated in 2017. Allen was an honorable mention all-conference pick as a junior, but he finished 72nd in the country in passing efficiency by completing just 56.3 percent of his passes (152-of-270) for just 1,812 yards and 16 touchdowns against six interceptions. Allen struggled against Power Five foes Iowa (23-of-40, 174 yards, 2 INT) and Oregon (9-of-24, 64 yards, INT). He missed the last two regular season games with an injury to his throwing shoulder but returned for the Cowboys' bowl win over Central Michigan (11-of-19, 154 yards, 3 TDs, 0 INT).