Born in Talavera de la Reina, Castile-La Mancha, Bautista rode a motorcycle for the first time at three years of age. His father owned a motorcycle repair shop and built his first bike from scratch; Bautista competed in his first race five years later. In only his second season he finished runner-up in the Madrid Minimoto Championship and then went on to win the championship three years in a row. In 1997 he simultaneously raced in the 50cc Aprilia Cup where he claimed his first podium, finishing the season in 6th place.