Villegas came to the United States at an early age, and played a year of college soccer at Kean College. His first taste of Major League Soccer action came in 1996, when he played three games for the MetroStars while on loan from the New Jersey Stallions of the USISL.  Three years in the minors followed, until the Metros drafted Villegas in the first round of the 1999 MLS Supplemental Draft. He would play the next four and a half seasons for the Metros, mostly as a right midfielder, but also some as a forward and a defender. Villegas was traded to D.C. United midway through the 2002 season. He would spend the rest of the year with DC, scoring two goals and adding five assists. Villegas left MLS afterwards, going back to his native Ecuador to play for Barcelona SC, ESPOLI, Manta and Cuenca.  In 2005, he came back to the U.S., signing with the Puerto Rico Islanders, which he will repeat in 2006.