[2] Vélez was drafted by the MetroStars in the 2003 MLS SuperDraft, but decided to sign with the Seattle Sounders of the USL First Division instead of playing in Major League Soccer.

Vélez signed with the Puerto Rico Islanders in 2005, where he scored 2 goals in 22 games playing as a defender.

During the 2006 season, Vélez was instrumental in the Islanders' run to the playoffs and their qualification for the CONCACAF Champions Cup, the first time in team history they had qualified for either tournament.

His everyday play as defender was crucial to the Islanders advancing for the first time in team history to the USL Semi-Finals.

[5] Toronto FC released Marco on August 13, 2009[6] and returned to his former club Puerto Rico Islanders.

[13] In December 2018, Amado Guevara confirmed that Marco Vélez will coach the Puerto Rico national under-17 football team during 2019 World Cup Qualification.