Bautista joined the Letran Squires basketball team in 2000, forming a formidable lineup which made them a force to reckon in the NCAA Juniors division.

Teaming up with then MVP Ronjay Enrile, Ira Buyco, Billy Ray Anabo, Mark Balneg and Wilbert Soriano the Squires swept the elimination round with a 14-0 record and give them an automatic trip to the Juniors finals with a twice-to-beat advantage.

When Toyota-Otis and Letran made a partnership to send the Knights in the PBL, he and superstar teammate Ronjay Enrile became founding stars of the team.

The Knights lost to Harbour Centre Port Masters 3-2 led by very close friend LA Tenorio and Joseph Yeo.

Boyet Bautista was also included in the National Team that won the Philippines a gold medal at the Southeast Asian Games in Thailand in December 2007.