Boise State (13-4, 4-0 Mountain West) has now tied a school record with 10-straight wins. The Broncos remain in a first-place tie with San Diego State which beat Colorado State on Wednesday.
Thompson made two free throws to give the Broncos a 63-49 lead with 4:01 to play. But Marqueze Coleman went on his own 9-0 run, and D.J. Fenner's layup brought Nevada to within 63-60 with 1:12 to go.
The Broncos' Nick Duncan drilled a 3, Thompson hit two more free throws and Anthony Drmic made four-straight free throws to end Nevada's threat.
Nevada (10-7, 2-3) got 17 points from Coleman and Fenner added 13.
The Wolfpack committed 25 fouls and Boise State went 26 of 36 from the line.
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