Vagenas graduated from Saint Francis High School in La Cañada Flintridge, class of 1996, where he played for coach Glen Appels and captained the team to a CIF Southern Section Championship his senior year, as well as being named CIF SS divisional player of the year.

He played college soccer at UCLA from 1996 to 1999, leading them to the NCAA title in 1997, and finished his career there with 15 goals and 30 assists in 82 games.

He was a fan favorite with Galaxy due to his energetic play and local roots (earning him the nickname "Pasadena Pete").

Vagenas became a free agent in Major League Soccer when he was not selected in the Re-Entry draft; after a couple of months out of the game he signed for expansion side Vancouver Whitecaps FC in April 2011.

He earned his first cap for the senior national team on October 25, 2000, against Mexico, but injuries have curtailed his appearances at the international level.