The 2006 MLS SuperDraft, held in Philadelphia on January 20, 2006, was the seventh incarnation of the annual Major League Soccer SuperDraft. The first selection originally belonged to Chivas USA, but they traded it to the MetroStars for the fifth overall selection and Jason Hernandez. The MetroStars then drafted Marvell Wynne. The draft was followed by the 2006 MLS Supplemental Draft. The draft has produced multiple United States men's national soccer team players, including Sacha Kljestan, Jozy Altidore (2nd round), and Jonathan Bornstein (4th round).

Player selection

Round one

Round one trades

Round two

Round two trades

Round three

Round three trades

Round four

Round four trades