| Season: | 1999 |
| Winners: | Minnesota Thunder (1st title) |
| Premiers: | Rochester Rhinos (2nd title) |
| League Topscorer: | Niall Thompson, Mark Baena (20 goals) |
| Nextseason: | 2000 |
The 1999 USL A-League was an American Division II league run by the United Soccer League during the summer of 1999.
The Hershey Wildcats advanced to the Eastern Conference finals.
The Rochester Rhinos advanced to the Eastern Conference finals.
The Minnesota Thunder advanced to the Western Conference final.
The San Diego Flash advanced to the Western Conference final.
The Rochester Rhinos advanced to the final.
The Minnesota Thunder advanced to the final.
MVP: Amos Magee, Minnesota Thunder
| Rank | Scorer | Club | Goals | Assists | Points |
|---|---|---|---|---|---|
| 1 | Niall Thompson | Vancouver 86ers | 20 | 7 | 47 |
| 2 | Mark Baena | Seattle Sounders | 20 | 6 | 46 |
| Eduardo Sebrango | Vancouver 86ers | 18 | 10 | 46 | |
| 4 | Darko Kolic | Long Island Rough Riders | 17 | 9 | 43 |
| 5 | Steve Patterson | Orange County Zodiac | 19 | 4 | 42 |
| 6 | Jamel Mitchell | Hershey Wildcats | 15 | 9 | 39 |
| Ernest Inneh | Staten Island Vipers | 18 | 3 | 39 | |
| 8 | Greg Simmonds | Hershey Wildcats | 16 | 6 | 38 |
| 9 | Onandi Lowe | Richmond Kickers | 15 | 7 | 37 |
| John Wolyniec | Long Island Rough Riders | 15 | 7 | 37 | |
| John Sulentic | Vancouver 86ers | 9 | 19 | 37 | |
| 12 | Carlos Farias | San Diego Flash | 15 | 6 | 36 |
| Ian Russell | Seattle Sounders | 14 | 8 | 36 | |
| 14 | Gary Glasgow | Richmond Kickers | 14 | 7 | 35 |
| 15 | Patrick Beech | New Orleans Storm | 16 | 2 | 34 |
| 16 | Paul Conway | Charleston Battery | 14 | 5 | 33 |
| 17 | Dan Stebbins | Milwaukee Rampage | 10 | 12 | 32 |
| 18 | Mac Cozier | Jacksonville Cyclones | 13 | 4 | 30 |
| Gustavo Leal | Orange County Zodiac | 13 | 4 | 30 | |
| Mugurel Dumitru | San Diego Flash | 9 | 12 | 30 |