The A-League serves as a type of minor league system for Major League Soccer. The division II outdoor league is part of the United Systems of Independent Soccer Leagues (USISL) and is recognized by U.S. Soccer. MLS and the USISL have an agreement where MLS teams can assign players to the A-League and call-up A-League players when desired. Also, the U.S. Pro-40 Select team is made-up of players from the MLS's Project 40 program. Project 40 is a joint venture between MLS and U.S. Soccer aimed at developing young American players, giving them the chance to train with MLS clubs and play games at various professional levels. The U.S. Pro-40 team played all their games on the road.
Eastern Conference
| | Northeast Division | W | L | Pts | GF | GA |
|---|
| * | Rochester Raging Rhinos | 22 | 6 | 92 | 47 | 20 |
| † | Staten Island Vipers | 19 | 9 | 82 | 52 | 31 |
| † | Long Island Rough Riders | 18 | 10 | 74 | 57 | 44 |
| † | Pittsburgh Riverhounds | 16 | 12 | 72 | 63 | 43 |
| † | Lehigh Valley Steam | 15 | 13 | 63 | 42 | 44 |
| | Boston Bulldogs | 12 | 16 | 61 | 49 | 36 |
| | Toronto Lynx | 12 | 16 | 51 | 31 | 37 |
| | Connecticut Wolves | 7 | 21 | 34 | 32 | 68 |
| | Atlantic Division | W | L | Pts | GF | GA |
|---|
| * | Hershey Wildcats | 17 | 11 | 75 | 54 | 33 |
| † | Richmond Kickers | 17 | 11 | 69 | 51 | 44 |
| † | Charleston Battery | 15 | 13 | 68 | 50 | 34 |
| | Atlanta Silverbacks | 15 | 13 | 62 | 43 | 39 |
| | Jacksonville Cyclones | 16 | 15 | 59 | 51 | 61 |
| | Hampton Roads Mariners | 15 | 13 | 57 | 45 | 41 |
| | Raleigh Capital Express | 11 | 17 | 47 | 32 | 50 |
| | Maryland Mania | 3 | 25 | 13 | 16 | 85 |
Western Conference
| | Central Division | W | L | Pts | GF | GA |
|---|
| * | Minnesota Thunder | 22 | 6 | 88 | 57 | 17 |
| † | U.S. Pro-40 | 17 | 11 | 66 | 44 | 46 |
| † | New Orleans Storm | 14 | 14 | 66 | 56 | 61 |
| | Indiana Blast | 13 | 15 | 55 | 43 | 51 |
| | Milwaukee Rampage | 13 | 15 | 54 | 44 | 49 |
| | Tennessee Rhythm | 11 | 17 | 49 | 44 | 52 |
| | Cincinnati Riverhawks | 7 | 21 | 34 | 45 | 71 |
| | Pacific Division | W | L | Pts | GF | GA |
|---|
| * | San Diego Flash | 20 | 8 | 90 | 65 | 30 |
| † | Vancouver 86ers | 19 | 9 | 84 | 77 | 31 |
| † | Seattle Sounders | 19 | 9 | 81 | 56 | 36 |
| † | Orange County Zodiac | 17 | 11 | 73 | 59 | 49 |
| † | El Paso Patriots | 12 | 16 | 55 | 49 | 59 |
| | San Francisco Bay Seals | 9 | 19 | 40 | 37 | 54 |
| | Sacramento Geckos | 0 | 28 | 1 | 16 | 91 |
Note: Three points are awarded for a victory in regulation or overtime. One point is awarded for a shootout win. Shootouts occur if a game is tied after a 15-minute sudden-death overtime.
Playoffs
Round of 16 (Single elimination)
| Sept. 10 | Rochester 2, Lehigh Valley 1 | at Rochester |
| Sept. 10 | San Diego 3, El Paso 1 | at San Diego |
| Sept. 10 | U.S. Pro-40 3, Vancouver 1 | at Vancouver |
| Sept. 11 | Staten Island 3, Richmond 2 OT | at Staten Island |
| Sept. 11 | Hershey 3, Charleston 2 | at Hershey |
| Sept. 11 | Pittsburgh 4, Long Island 3 | at Long Island |
| Sept. 11 | Minnesota 4, New Orleans 0 | at Minnesota |
| Sept. 11 | Seattle 6, Orange County 3 | at Seattle |
Quarterfinals (Best of 3)
Eastern Conference
Hershey vs. Staten Island
| Sept. 16 | Hershey 2, Staten Island 0 | at Hershey |
| Sept. 18 | Hershey 2, Staten Island 0 | at Staten Island |
| Hershey wins series, 2-0 |
Rochester vs. Pittsburgh
| Sept. 18 | Rochester 6, Pittsburgh 2 | at Rochester |
| Sept. 25 | Pittsburgh 1, Rochester 0 | at Pittsburgh |
| Sept. 28 | Rochester 2, Pittsburgh 0 | at Rochester |
| Rochester wins series, 3-1 |
Western Conference
Minnesota vs. US Pro-40
| Sept. 18 | Minnesota 1, US Pro-40 0 OT | at Minnesota |
| Sept. 20 | Minnesota 2, US Pro-40 0 | at Minnesota |
| Minnesota wins series, 2-0 |
San Diego vs. Seattle
| Sept. 18 | San Diego 6, Seattle 0 | at San Diego |
| Sept. 25 | San Diego 1, Seattle 0 | at Seattle |
| San Diego wins series, 2-0 |
Semifinals (Best of 3)
Eastern Conference
Rochester vs. Hershey
| Oct. 3 | Hershey 2, Rochester 1 | at Hershey |
| Oct. 9 | Rochester 1, Hershey 0 | at Rochester |
| Oct. 11 | Rochester 3, Hershey 1 | at Rochester |
| Rochester wins series, 2-1 |
Western Conference
Minnesota vs. San Diego
| Oct. 2 | Minnesota 4, San Diego 1 | at Minnesota |
| Oct. 7 | Minnesota 2, San Diego 1 | at San Diego |
| Minnesota wins series, 2-0 |
Final
Oct. 16, 1999 at Blaine, Minn. Attendance: 9,987
| | 1 | 2— | F |
|---|
| Minnesota | 1 | 1— | 2 |
| Rochester | 0 | 1— | 1 |