During the 2007 season, Moore was redshirted.
As a redshirt freshman in 2008, Moore led the Broncos to an undefeated regular season and the WAC championship while throwing 25 touchdowns and 9 interceptions in 12 games. In the final game of 2008, Boise State lost to Texas Christian University (TCU) in the 2008 Poinsettia Bowl, the first of two consecutive meetings for the non-Automatic Qualifying rivals. He was named WAC Freshman of the Year and Second-team All-conference after spectacular first season, guiding Boise State to 12-1 record and was named Boise State’s Most Valuable Offensive Player by vote of teammates. He was named to Phil Steele Publications’ Second team All-WAC and also voted to the Football Writers Association of America’s freshman All-America team.
He ranked 12th in nation in passing efficiency and 24th in total offense, averaging 265.85 yards per game and was first in WAC in passing efficiency (157.1) and second in total offense (265.8) and average passing yards per game (268.2). He completed 281 of 405 passes for 3,486 yards with 25 touchdowns and 10 interceptions.
In January 2009, Moore was ranked as the 37th best returning player in college football by College Football News.
Moore threw for a school record 39 touchdowns with only 3 interceptions to lead the Broncos to a 14–0 record, another WAC title, and an at large bid to the Fiesta Bowl vs. undefeated #4 ranked TCU. The 2009 Fiesta Bowl was highly controversial due to the decision to pit the two non-Automatic Qualifying schools against each other instead of having them face Automatic Qualifying teams. The BCS was criticized for the perception that the risk of both, or either, team defeating a "power conference" team was too great, and that the BCS had TCU and BSU face each other so that the damage of their participation would be minimized. He finished the 2009 regular season with the highest passer efficiency rating in Division I-A with a rating of 167.3. In his first two years as a starting quarterback, Moore did not lose a regular season game.
Moore started the 2010 Fiesta Bowl against widely favored TCU and played the entire game. He had no interceptions, fumbles, or muffed snaps. He led the team on a 4th quarter 78-yard touchdown scoring drive to take the lead for good and win the game 17-10.
He was named First-team All-American by CBSSportsline.com, a subsidiary of CBS Sports. He was named one of ten finalists for the Manning Award. He was also First-team All-WAC and the WAC Offensive Player of the Year in 2009 and finished 7th in Heisman voting for 2009.
Kellen Moore led the Broncos to a 33–30 victory over Virginia Tech on September 6, 2010. The game was highly anticipated and received a 6.8 TV rating, nearly twice that of the next most highly watched game. Moore contributed 3 passing touchdowns in the game with a final game-winning strike to Austin Pettis with 1:14 remaining in the game. As a result of the victory, Boise State received 8 first place votes in the week 2 AP Poll, and it moved up to third in the Coaches' Poll. Moore was also mentioned by major sports media as a top candidate for the 2010 Heisman Trophy. After finishing the season with 3,506, 33 TD's and only 5 INT's, Moore was named a finalist for the Heisman Trophy and was invited to the ceremony in New York City to become the first ever Boise State player to be a Heisman finalist. Moore finished 4th in Heisman voting. Moore was also a finalist for the Davey O'Brien Award, the Maxwell Award, and the Manning Award (all won by Cam Newton). Moore was named the Touchdown Club of Columbus Quarterback of the Year. Boise State was invited to the 2010 Maaco Bowl Las Vegas, where they defeated Utah 26-3.
On March 28, 2011 the Sporting News named Moore as the #1 player in their annual list of the top 25 players in the nation. He is ranked ahead of Stanford quarterback Andrew Luck and Oregon running back LaMichael James who both finished ahead of Moore in the 2010 Heisman voting. He only needed 8 wins during the 2011 season to pass Colt McCoy for most wins by a quarterback in NCAA history. He threw his 100th touchdown pass against Georgia during week one. Following an opening season win against Georgia in the Chick-fil-A College Kickoff, Moore was featured on the cover of Sports Illustrated, distributed only in the west.
With the Broncos defeat of Air Force on October 22, he tied former Texas quarterback Colt McCoy for the career wins record with 45 wins. On November 5, the Broncos defeated UNLV and Moore broke the record to become the FBS leader in career wins for a starting quarterback at 46.
He was one of three finalists for the Maxwell Award along with Andrew Luck and Trent Richardson (won by Luck). For the second year in a row, he was named the Touchdown Club of Columbus Quarterback of the Year and it was annouced that beginning in 2012 the award will be known as the Kellen Moore Award. He currently is first in the FBS in completion percentage. With the Broncos' 56–24 rout of Arizona State in the 2011 Maaco Bowl Las Vegas, Moore became the first quarterback in FBS history to win 50 games in his career.