| School Name | API (2009) | API (2008) |
| Manchester Gate | 986 | 973 |
| Edison Computech | 927 | 913 |
| University High | 915 | 898 |
| Forkner Elementary | 885 | 866 |
| Gibson Elementary | 876 | 864 |
| Design Science Early College High | 874 | 822 |
| Bullard Talent Project | 864 | 849 |
| Malloch Elementary | 842 | 849 |
| Eaton Elementary | 840 | 832 |
| Baird Middle | 830 | 819 |
| KIPP Academy Fresno | 825 | 844 |
| Starr Elementary | 824 | 809 |
| McCardle Elementary | 812 | 792 |
| Figarden Elementary | 810 | 799 |
| Kratt Elementary | 791 | 772 |
| Tenaya Middle | 791 | 793 |
| Vinland Elementary | 788 | 741 |
| Birney Elementary | 783 | 759 |
| Robinson Elementary | 780 | 742 |
| Thomas Elementary | 780 | 754 |
| Holland Elementary | 778 | 764 |
| Akira Yokomi Elementary | 775 | 740 |
| Powers-Ginsburg Elementary | 772 | 733 |
| Fremont Elementary | 763 | 731 |
| Jackson Elementary | 762 | 742 |
| Bullard High | 760 | 763 |
| Ayer Elementary | 756 | 760 |
| Wolters Elementary | 750 | 710 |
| Ann B. Leavenworth | 747 | 704 |
| Hamilton Elementary | 744 | 735 |
| Wishon Elementary | 743 | 727 |
| Wilson Elementary | 738 | 684 |
| Ericson Elementary | 737 | 722 |
| Lawless Elementary | 737 | 714 |
| Ewing Elementary | 733 | 693 |
| Roeding Elementary | 730 | 710 |
| Deborah A. Williams Elementary | 729 | 683 |
| Viking Elementary | 729 | 710 |
| Molly S. Bakman Elementary | 727 | 695 |
| Erma Duncan Polytechnical High | 727 | 708 |
| Homan Elementary | 727 | 713 |
| Norseman Elementary | 727 | 707 |
| Jefferson Elementary | 726 | 665 |
| Lincoln Elementary | 726 | 682 |
| Edith B. Storey Elementary | 726 | 713 |
| Del Mar Elementary | 725 | 714 |
| Valley Preparatory Academy Charter | 721 | 699 |
| Sunset Elementary | 721 | 708 |
| Aynesworth Elementary | 720 | 705 |
| Easterby Elementary | 716 | 718 |
| Addams Elementary | 710 | 706 |
| Pyle Elementary | 710 | 683 |
| Turner Elementary | 710 | 692 |
| Winchell Elementary | 705 | 683 |
| David L. Greenberg Elementary | 698 | 704 |
| Edison High | 697 | 703 |
| Heaton Elementary | 695 | 696 |
| Slater Elementary | 694 | 699 |
| Ahwahnee Middle | 692 | 707 |
| Burroughs Elementary | 690 | 683 |
| Mayfair Elementary | 686 | 695 |
| Centennial Elementary | 685 | 652 |
| Miguel Hidalgo Elementary | 685 | 656 |
| Herbert Hoover High | 683 | 698 |
| Wawona Middle | 681 | 662 |
| Susan B. Anthony Elementary | 680 | 652 |
| Lowell Elementary | 677 | 633 |
| Fort Miller Middle | 677 | 660 |
| Calwa Elementary | 674 | 655 |
| King Elementary | 674 | 641 |
| Scandinavian Middle | 673 | 652 |
| Sunnyside High | 664 | 668 |
| Kings Canyon Middle | 664 | 637 |
| Mario G. Olmos Elementary | 663 | 635 |
| Webster Elementary | 662 | 641 |
| Muir Elementary | 661 | 652 |
| Valley Arts and Science Academy (VASA) | 658 | 636 |
| Elizabeth Terronez Middle | 656 | 649 |
| Ezekiel Balderas Elementary | 655 | 621 |
| Sierra Charter | 654 | 587 |
| Kirk Elementary | 654 | 622 |
| Rowell Elementary | 653 | 653 |
| Columbia Elementary | 642 | 606 |
| Sequoia Middle | 641 | 641 |
| Tioga Middle | 635 | 616 |
| Fresno High | 622 | 596 |
| Tehipite Middle | 622 | 609 |
| Irwin O. Addicot Elementary | 622 | 643 |
| Cooper Middle | 620 | 567 |
| Roosevelt High | 611 | 568 |
| McLane High | 610 | 611 |
| Florence E. Rata | 605 | 515 |
| Yosemite Middle | 587 | 587 |
| Carver Academy | 580 | 576 |
| School of Unlimited Learning | 544 | 538 |
| Cambridge Continuation High | 501 | 546 |
| J. E. Young Academic Center | 500 | 544 |
| Carter G. Woodson Public Charter | 482 | 536 |
| New Millenium Charter | 447 | 404 |
| Fresno Prep Academy | 447 | 456 |
| Dewolf Continuation High | 446 | 434 |
| Academy for New Americans | | |
| Fresno Adult | | |
| Lane Elementary | | |
| Fulton Special Education | | |
| Phoenix Elementary Academy Community Day | | |