Aguayo was signed by the Philadelphia Phillies as an amateur free agent on December 27, 1975, at the age of 16.

Although Aguayo would play with the Phillies until 1988, he only appeared in two games in the 1981 postseason, acting as a pinch runner in the series against the Dodgers.

[4] Aguayo was traded to the New York Yankees in the middle of July 1988 for minor leaguer Amalio Carreño, and would sign with the Cleveland Indians after the season.

On October 23 of that season, the Mets announced that Aguayo would be reassigned within the organization and that Razor Shines would be replacing him as third base coach.

Aguayo is currently the international field coordinator/infield instructor for the minor league staff of the St. Louis Cardinals.