The 1999 Major League Soccer College Draft was held on February 6 and 7, 1999 in Fort Lauderdale, Florida. The first round of the draft took place on February 6 with the second and third rounds on February 7. The College Draft was followed by the 1999 MLS Supplemental Draft later on February 7.

Round 1

{| class="wikitable sortable" style="width:80%"

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!width=7%| Pick # !!width=27%| MLS team !!width=24%| Player !!width=10%| Position !!width=33%| Affiliation

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! 1

| D.C. United || Jason Moore || M || University of Virginia

|-

! 2

| Miami Fusion