| School Name | API (2009) | API (2008) |
| Mission San Jose Elementary | 993 | 988 |
| William Hopkins Junior High | 992 | 987 |
| Joshua Chadbourne Elementary | 988 | 978 |
| John Gomes Elementary | 984 | 981 |
| Fred E. Weibel Elementary | 973 | 971 |
| Forest Park Elementary | 964 | 966 |
| James Leitch Elementary | 959 | 954 |
| Mission Valley Elementary | 956 | 945 |
| Mission San Jose High | 948 | 931 |
| Ardenwood Elementary | 941 | 915 |
| Warm Springs Elementary | 936 | 929 |
| Parkmont Elementary | 927 | 928 |
| Niles Elementary | 897 | 882 |
| Steven Millard Elementary | 890 | 861 |
| John M. Horner Junior High | 883 | 874 |
| Warwick Elementary | 872 | 863 |
| Thornton Junior High | 868 | 837 |
| Brookvale Elementary | 867 | 828 |
| Glenmoor Elementary | 864 | 847 |
| Oliveira Elementary | 856 | 811 |
| John G. Mattos Elementary | 852 | 842 |
| Harvey Green Elementary | 848 | 834 |
| Patterson Elementary | 848 | 813 |
| O. N. Hirsch Elementary | 846 | 835 |
| Centerville Junior High | 835 | 817 |
| Irvington High | 830 | 792 |
| Tom Maloney Elementary | 827 | 817 |
| Brier Elementary | 819 | 837 |
| G. M. Walters Junior High | 808 | 782 |
| Joseph Azevada Elementary | 806 | 833 |
| Vallejo Mill Elementary | 806 | 831 |
| E. M. Grimmer Elementary | 800 | 762 |
| Cabrillo Elementary | 799 | 758 |
| American High | 787 | 782 |
| Washington High | 776 | 776 |
| John Blacow Elementary | 775 | 769 |
| Circle of Independent Learning | 737 | 735 |
| J. Haley Durham Elementary | 734 | 773 |
| John F. Kennedy High | 711 | 706 |
| Vista Alternative | 710 | 677 |
| Robertson High (Continuation) | 459 | 461 |
| Fremont Adult | | |