| School Name | API |
| John Gomes Elementary | 988 |
| Mission San Jose Elementary | 985 |
| Joshua Chadbourne Elementary | 975 |
| William Hopkins Junior High | 965 |
| Fred E. Weibel Elementary | 965 |
| Forest Park Elementary | 958 |
| Warm Springs Elementary | 929 |
| Mission Valley Elementary | 928 |
| Mission San Jose High | 927 |
| James Leitch Elementary | 926 |
| Parkmont Elementary | 921 |
| Ardenwood Elementary | 919 |
| Niles Elementary | 887 |
| Brookvale Elementary | 860 |
| Steven Millard Elementary | 860 |
| Glenmoor Elementary | 857 |
| Warwick Elementary | 855 |
| John M. Horner Junior High | 845 |
| Joseph Azevada Elementary | 826 |
| Thornton Junior High | 823 |
| Brier Elementary | 819 |
| John G. Mattos Elementary | 808 |
| Tom Maloney Elementary | 807 |
| Irvington High | 804 |
| O. N. Hirsch Elementary | 801 |
| Patterson Elementary | 798 |
| Oliveira Elementary | 792 |
| Vallejo Mill Elementary | 790 |
| Circle of Independent Learning | 785 |
| Harvey Green Elementary | 767 |
| E. M. Grimmer Elementary | 762 |
| American High | 761 |
| John Blacow Elementary | 751 |
| Washington High | 747 |
| J. Haley Durham Elementary | 744 |
| G. M. Walters Junior High | 744 |
| Vista Alternative | 743 |
| Cabrillo Elementary | 724 |
| John F. Kennedy High | 689 |
| Robertson High (Continuation) | 443 |
| Fremont Adult | |
| Centerville Junior High | |