Bautista was appointed as the head coach of the Philippine women's national football team in April 2015 becoming the first woman to lead the women's senior national team of the Philippines.[5][6]
Bautista returns as the head coach of the Philippine women's national team by June 2018 and guided the team in the 2018 AFF Women's Championship.[11] Like in her first national team stint, she was again succeeded by Marnelli Dimzon in August 2018.[12]