Harper's scores on 18 carries marked the third time in four games the redshirt senior has found the end zone twice for the Broncos (7-1, 4-0 MWC), who logged their seventh straight victory.
Shane Williams-Rhodes and Jay Ajayi also scored, while Joe Southwick went 20-of-28 passing for 202 yards with an interception for Boise State.
The Cowboys (1-7, 0-4) were led by Brett Smith, who completed 24-of-35 passes for 216 yards and rushed for 59 yards with two scores.
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