Aguilar was a seven-letter athlete in baseball and football for the Texans. In football, he was an all-district wide receiver and defensive back. A pitching standout, Aguilar helped the Rayburn team reach the 1985 state championship game under Coach Al Campo Sr.. He was named the All-Greater Houston team's player of the year as a senior, having already earned a spot on the team as a junior.

Following his graduation, Aguilar started and won the prestigious North-South All-Star Game. He then played four seasons for the Baylor Bears from 1986 to 1989, being named the team's most valuable player in 1987 and tying for the team lead with seven wins in 1988.