Boise State scored 21 straight points, recovering a pooch kickoff in the process and taking a 40-34 lead with 7:04 remaining.
The Bulldogs then used 13 plays to drive down the field and pull out a win that boosted their record to 3-0. It was the first Mountain West Conference game for Fresno State.
Derek Carr threw 60 times for the Bulldogs, completing 39 of them for 460 yards and four touchdowns.
That effort, however, seemed likely to come up short when Boise State's Joe Southwick helped put together the late Boise State comeback.
Aaron Baltazar began the rally with a 35-yard touchdown run with 41 seconds remaining in the third period, Baltazar scored again on a 2-yard run at the end of a 13-play drive and Southwick scored on a 1-yard plunge after the Broncos recovered the ensuing kickoff.
Southwick went 31-of-45 for 313 yards without a touchdown. Boise State fell to 2-2 and is 1-1 in league play.