The 2003 MLS Superdraft was held January 17, 2003 in Kansas City, Missouri. It was the fifth annual SuperDraft held by Major League Soccer.
Player selection
thumb|The [[New York Red Bulls|MetroStars selected Ricardo Clark second overall. A 3x MLS All-Star, he was named to the 2006 MLS Best XI. Clark earned 34 caps with the US Men's National Team and was selected to the 2010 FIFA World Cup squad.]]
thumb|The [[New York Red Bulls|MetroStars selected Mike Magee 4th overall. in 2013, he was won the Major League Soccer MVP and was named to the MLS Best XI.]]
thumb|[[San Jose Earthquakes|San Jose selected Todd Dunivant 6th overall. He was named to the 2011 MLS Best XI.]]
;Key
{| class="wikitable"
| style="background:#FFCC00"|*
| Denotes a player contracted under the Project-40 program
|-
| style="background:#CFECEC"| ^
| Denotes player who has been selected to an MLS All-Star Game
|-
| style="background:#CCFF99"|§
| Denotes a player who won the MLS Rookie of the Year
|-
| style="background: #FBCEB1"| †
| Denotes player who has been selected for an MLS Best XI team
|-
| style="background:#FFFF99"| ~
|Denotes a player who won the MLS MVP
|-
|}
Round One
{| class="wikitable sortable"
|-
!width=7%| Pick # !!width=30%| MLS team !!width=22%| Player !!width=10%| Position !! Affiliation
|-
! 1
| D.C. United || style="background:#CFECEC"|Alecko Eskandarian*^ || F || University of Virginia
|-
! 2
| MetroStars || bgcolor="#FBCEB1"| Ricardo Clark*^† || M || Furman University
|-
! 3
| Chicago Fire