| Fremont Unified School District | 2013 API | 2012 API |
| Mission San Jose Elementary | 995 | 996 |
| John Gomes Elementary | 991 | 990 |
| William Hopkins Junior High | 986 | 986 |
| Forest Park Elementary | 985 | 974 |
| Warm Springs Elementary | 978 | 967 |
| Joshua Chadbourne Elementary | 975 | 981 |
| Fred E. Weibel Elementary | 969 | 971 |
| Ardenwood Elementary | 965 | 961 |
| Mission Valley Elementary | 960 | 968 |
| James Leitch Elementary | 959 | 987 |
| Parkmont Elementary | 951 | 953 |
| Mission San Jose High | 951 | 951 |
| O. N. Hirsch Elementary | 928 | 903 |
| Niles Elementary | 925 | 909 |
| John M. Horner Junior High | 920 | 929 |
| Warwick Elementary | 907 | 895 |
| Brookvale Elementary | 905 | 897 |
| Thornton Junior High | 903 | 886 |
| John G. Mattos Elementary | 892 | 882 |
| Harvey Green Elementary | 890 | 872 |
| Glenmoor Elementary | 889 | 882 |
| Oliveira Elementary | 888 | 888 |
| Steven Millard Elementary | 887 | 894 |
| Irvington High | 884 | 874 |
| Tom Maloney Elementary | 874 | 854 |
| Brier Elementary | 859 | 862 |
| Patterson Elementary | 858 | 859 |
| Centerville Junior High | 855 | 855 |
| Joseph Azevada Elementary | 855 | 826 |
| J. Haley Durham Elementary | 844 | 865 |
| American High | 842 | 831 |
| Vallejo Mill Elementary | 837 | 836 |
| E. M. Grimmer Elementary | 820 | 818 |
| John Blacow Elementary | 815 | 835 |
| Cabrillo Elementary | 811 | 810 |
| Circle of Independent Learning | 807 | 795 |
| G. M. Walters Junior High | 796 | 808 |
| Washington High | 792 | 790 |
| John F. Kennedy High | 743 | 750 |
| Vista Alternative | 733 | 651 |
| Robertson High (Continuation) | 619 | 542 |