In his redshirt freshman year in 1999, Kingsbury appeared in six games, starting the season finale against Oklahoma. He completed 25 of 57 passes for 492 yards, four touchdowns and an interception in his initial collegiate season. In 2000, he assumed the starting role and connected on 361 of 584 passes for 3,412 yards, 21 touchdowns and 17 interceptions. He added two scores on 78 carries. His season ended with a loss to the East Carolina Pirates in the Gallery-Furniture.com Bowl, with a final score of 40-27. As a junior in 2001, Kingsbury was an All-District first-team selection and All-Big 12 Conference second-team pick by the league's coaches for his performance. He completed 364 of 528 passes for 3,502 yards, 25 touchdowns and only nine interceptions.