Boise State (2-1) forced five turnovers and held the Cougars (2-2) to 200 total yards. The Cougars were held scoreless until the final minutes of the game when backup freshman quarterback Taysom Hill scored on a 4-yard run.
But with 3:37 remaining, BYU coach Bronco Mendenhall elected to go for the win and the Cougars' first-ever victory over Boise State. But Hill's pass on the run was deflected by a defender and fell incomplete in the end zone.
The Broncos, helped by a long kick return, ran out the clock to notch their third straight victory over the Cougars.
Boise State's offense wasn't much better, managing just 261 yards. Running back D.J. Harper led the way, rushing for 112 yards on 31 carries. Joe Southwick struggled again, especially on third and fourth downs. Southwick was 15 of 25 for 145 yards.
Boise State failed five times on fourth down attempts, with most of those coming in BYU territory and after Michael Frisina missed a 33-yard field goal attempt in the first quarter.
After a scoreless first half, Atkinson finally put some points on the board. On BYU's first possession of the second half, Atkinson dropped back in pass coverage and stepped in front of Riley Nelson's short pass. Atkinson then rumbled 36 yards for a touchdown to put Boise State up 7-0 at the 13:24 mark.
Nelson was benched after throwing his third interception of the game on BYU's next possession and replaced by Hill, who grew up in Pocatello, Idaho, and was recruited by Boise State.
Hill's legs finally provided the Cougars with a spark on offense. On BYU's final possession, Hill engineered an 11-play, 95-yard drive that was helped early by a Boise State personal foul. Hill was 3 of 5 on the drive and rushed for 39 yards.
For the game, Hill was 4 of 10 for 42 yards and he led the Cougars with 72 yards on 12 carries.