Here is the 1999 San Jose Clash schedule. Please note that all times are PT and that the schedule is subject to change.
| Date | Opponent | Time (PT) |
| Sat. March 20 | Chicago | 8:00 p.m. |
| Sat. March 27 | Colorado | 7:00 p.m. |
| Sat. April 3 | Los Angeles | 7:00 p.m. |
| Sat. April 10 | at Kansas City | 12:30 p.m. |
| Sat. April 17 | at D.C. United | 4:30 p.m. |
| Sat. April 24 | at Los Angeles | 7:30 p.m. |
| Fri. April 30 | Dallas | 7:30 p.m. |
| Sun. May 9 | Columbus | 2:00 p.m. |
| Sat. May 15 | at Dallas | 5:30 p.m. |
| Sat. May 22 | Dallas | 8:00 p.m. |
| Thu. May 27 | at Colorado | 6:30 p.m. |
| Thu. June 3 | Colorado | 7:30 p.m. |
| Sat. June 12 | Tampa Bay | 7:30 p.m. |
| Sat. June 19 | at Chicago | 5:00 p.m. |
| Sat. June 26 | at Miami | 4:30 p.m. |
| Wed. June 30 | at Columbus | 4:30 p.m. |
| *Sun. July 4 | D.C. United | 4:00 p.m. |
| Thu. July 8 | at Tampa Bay | 4:30 p.m. |
| Fri. July 23 | at Chicago | 5:00 p.m. |
| Sat. July 31 | at Kansas City | 5:30 p.m. |
| Sat. Aug. 7 | Los Angeles | 7:30 p.m. |
| Thu. Aug. 12 | at New England | 4:30 p.m. |
| Sat. Aug. 21 | New England | 7:30 p.m. |
| Sat. Aug. 28 | MetroStars | 7:30 p.m. |
| Wed. Sept. 1 | at Los Angeles | 7:30 p.m. |
| Sat. Sept. 4 | Kansas City | 7:30 p.m. |
| Sat. Sept. 11 | at Dallas | 5:30 p.m. |
| Sun. Sept. 19 | Miami | 2:00 p.m. |
| Wed. Sept. 22 | at MetroStars | 4:30 p.m. |
| Sun. Sept. 26 | Chicago | 2:00 p.m. |
| Fri. Oct. 1 | at Colorado | 6:00 p.m. |
| Wed. Oct. 6 | Kansas City | 7:30 p.m. |