Junior quarterback Riley Nelson will start for BYU on Saturday against San Jose State.
Coach Bronco Mendenhall announced the change from sophomore Jake Heaps on Friday.
Both played in last week's 27-24 win over Utah State, but Nelson was much more effective.
He led the Cougars (3-2) on a 96-yard drive that ended with a deflected pass for a touchdown with 11 seconds to play that capped a rally from 24-13.
Nelson, who has played in all five games, is 13 of 21 (61.9 percent) for 182 yards and two touchdowns without an interception. Heaps is 100 for 135 (54.1 percent) for 962 yards and three touchdowns but he has thrown five interceptions.