| Year | Men | Points | Women | Points |
| 2006 | Stanford | 1803.5 | BYU | 1088 |
| 2005 | Stanford | 1819 | Stanford | 1760.5 |
| 2004 | Stanford | 1595 | Stanford | 1211.5 |
| 2003 | Stanford | 1885 | Oregon State | 1069 |
| 2002 | Brigham Young | 1205 | Pacific | 1383 |
| 2001 | Stanford | 1610 | Pacific | 1296 |
| 2000 | USC | 1134 | USC | 988 |
| 1999 | UC Santa Barbara | 1208.5 | Nevada | 928 |
| 1998 | Florida | 1306 | BYU | 1075.5 |
| 1997 | California | 1177 | California | 1233.5 |
| 1996 | Stanford | 1395.5 | UCLA | 1585 |
| 1995 | Wisconsin | 638 | Arizona | 730 |
| 1994 | Stanford | 841 | UCLA | 702.5 |
| 1993 | Stanford | 1010 | UC Santa Barbara | 590.5 |
| 1992 | California | 911.5 | California | 798 |
| 1991 - No results available | ||||
| 1990 | Arizona State | 1111 | California | 1249.5 |
| 1989 - No results available | ||||
Note: The Nike Cup was hosted by the University of Southern California from 1989-1991 as the United States National Grand Prix Swimming Invitational and in 1992 as the Speedo Cup. The Nike Cup was known as the Speedo Cup through the 2006 meet. UC Irvine has hosted the meet since 1993.
