In 1989, he transferred to Santa Clara University where he spent the next two seasons. In 1989, Baichers first year with the Broncos, the team won the NCAA championship title against Virginia after the two schools played even through four overtimes. 1989 Baicher was named NCAA player of the year and was scouted by Manchester United and the US National Team.
Baicher switched to Santa Clara University in 1989 and spent the next couple of years there. The following season, his first with the Broncos, ended with a thrilling championship win over Virginia after four overtime periods. Baicher's outstanding performance earned him NCAA player of the year honors, and he was also sought after by Manchester United and the US National Team.