| School Name | API (2009) | API (2008) |
| Chaparral Elementary | 939 | 921 |
| Bathgate Elementary | 934 | 914 |
| Laguna Niguel Elementary | 929 | 890 |
| Ladera Ranch Elementary | 920 | 887 |
| Tijeras Creek Elementary | 920 | 896 |
| Wagon Wheel Elementary | 919 | 879 |
| Arroyo Vista Elementary | 912 | 887 |
| Vista del Mar Elementary | 910 | 892 |
| Ladera Ranch Middle | 909 | 880 |
| Don Juan Avila Elementary | 905 | 871 |
| Castille Elementary | 904 | 866 |
| Don Juan Avila Middle | 904 | 876 |
| John Malcom Elementary | 902 | 886 |
| Philip J. Reilly Elementary/Special Education | 901 | 862 |
| Las Flores Middle | 900 | 880 |
| Canyon Vista Elementary | 899 | 885 |
| Moulton Elementary | 896 | 876 |
| Las Flores Elementary | 896 | 875 |
| George White Elementary | 895 | 861 |
| Truman Benedict Elementary | 887 | 847 |
| Aliso Viejo Middle | 886 | 875 |
| Arroyo Vista Middle | 885 | 879 |
| Oso Grande Elementary | 884 | 877 |
| Bernice Ayer Middle | 883 | 866 |
| Marian Bergeson Elementary | 878 | 858 |
| Newhart Middle | 876 | 840 |
| Vista del Mar Middle | 874 | 812 |
| Concordia Elementary | 870 | 823 |
| Richard Henry Dana Elementary | 869 | 836 |
| Carl Hankey Elementary | 867 | 817 |
| Carl Hankey Middle | 865 | 817 |
| Barcelona Hills Elementary | 863 | 847 |
| Hidden Hills Elementary | 862 | 809 |
| Oak Grove Elementary | 860 | 857 |
| Niguel Hills Middle | 858 | 832 |
| Tesoro High | 855 | 836 |
| Palisades Elementary | 855 | 854 |
| Aliso Niguel High | 851 | 825 |
| Capistrano Home Outreach Option for Student Educat | 850 | 760 |
| Clarence Lobo Elementary | 848 | 803 |
| Dana Hills High | 839 | 825 |
| Crown Valley Elementary | 833 | 783 |
| Harold Ambuehl Elementary | 832 | 834 |
| San Clemente High | 828 | 817 |
| Shorecliffs Middle | 825 | 807 |
| Capistrano Valley High | 821 | 812 |
| Wood Canyon Elementary | 816 | 803 |
| Journey | 816 | 714 |
| Marblehead Elementary | 814 | 822 |
| San Juan Hills High | 810 | 748 |
| Del Obispo Elementary | 792 | 767 |
| Las Palmas Elementary | 790 | 719 |
| Marco Forster Middle | 781 | 778 |
| Viejo Elementary | 779 | 797 |
| Capistrano Connections Academy Charter | 773 | 750 |
| Kinoshita Elementary | 754 | 704 |
| Richard Henry Dana Exceptional Needs | 719 | 658 |
| San Juan Elementary | 686 | 670 |
| Opportunities for Learning | 685 | 718 |
| Junipero Serra High | 568 | 529 |
| Bridges Community Day | | |
| Capistrano Unified Adult Education Program | | |