Ajayi attended and played college football for Boise State from 2011 to 2014. He was redshirted as a true freshman at Boise State University in 2011. In October 2011, he was arrested for shoplifting after stealing a pair of sweatpants at a local Walmart and was later sentenced to five days in jail. As a redshirt freshman in 2012, he played in 11 games. He had 82 rushes for 548 yards and four touchdowns, including 118 yards and a touchdown on just six carries against New Mexico in his second career game. As a sophomore in 2013, he started 12 of 13 games and rushed for 100+ yards in six of them, including 24 carries for 222 yards and three touchdowns in game seven against Nevada. He ended the season having carried the ball 249 times for 1,425 yards and 18 touchdowns. As a junior in 2014, he became the first Boise State player to rush for 100+ yards in 10 games in a season, including two 200+ yard performances against Colorado State and Utah State. He ended his season with a 134-yard, three touchdown performance in the Broncos' 38–30 victory over the Arizona Wildcats in the 2014 Fiesta Bowl. He finished the season ranked fifth in the nation with a school-record 1,823 rushing yards and second nationally only to Wisconsin's Melvin Gordon with 28 rushing touchdowns (also a school record). Ajayi finished his final season at Boise State having accounted for 41. 3% of the team's total yards and touchdowns, third among running back prospects entering the 2015 NFL Draft, trailing only Melvin Gordon and Indiana's Tevin Coleman. He was named a first-team All-Mountain West Conference selection for the second consecutive season and earned third-team All-American honors by the Associated Press.