| School Name | API (2009) | API (2008) |
| Rio Calaveras Elementary | 833 | 814 |
| Commodore Stockton Skills | 828 | 811 |
| Kohl Open Elementary | 789 | 753 |
| Rosa Parks Academy | 775 | 737 |
| George W. Bush Elementary | 771 | 768 |
| San Joaquin Elementary | 756 | 747 |
| Wilson Elementary | 748 | 741 |
| Hazelton Elementary | 738 | 746 |
| Weber Institute | 729 | 685 |
| Victory Elementary | 728 | 707 |
| Pulliam Elementary | 725 | 701 |
| Institute of Business, Management, and Law Charter | 723 | 715 |
| John Marshall Elementary | 710 | 712 |
| Grunsky Elementary | 710 | 711 |
| Maxine Hong Kingston Elementary | 701 | 726 |
| Fillmore Elementary | 698 | 690 |
| Valenzuela Elementary | 698 | 725 |
| Walton Development Center | 696 | 666 |
| Dolores Huerta Elementary | 696 | 712 |
| California Virtual Academy at San Joaquin | 694 | 672 |
| Elmwood Elementary | 693 | 682 |
| Hoover Elementary | 690 | 683 |
| Tyler Skills Elementary | 686 | 670 |
| Madison Elementary | 676 | 682 |
| Adams Elementary | 675 | 654 |
| Monroe Elementary | 675 | 669 |
| El Dorado Elementary | 674 | 668 |
| Taft Elementary | 673 | 662 |
| George Washington Elementary | 673 | 685 |
| Valentine Peyton Elementary | 668 | 613 |
| King Elementary | 668 | 652 |
| Montezuma Elementary | 668 | 645 |
| Cleveland Elementary | 667 | 663 |
| McKinley Elementary | 661 | 676 |
| Grant Elementary | 660 | 688 |
| Kennedy Elementary | 660 | 656 |
| Van Buren Elementary | 654 | 662 |
| Alexander Hamilton Elementary | 652 | 663 |
| John C. Fremont Elementary | 646 | 634 |
| Harrison Elementary | 644 | 674 |
| August Elementary | 641 | 661 |
| Wilhelmina Henry Elementary | 633 | 624 |
| Taylor Skills Elementary | 626 | 636 |
| Richard A. Pittman Elementary | 623 | 609 |
| Edison High | 610 | 589 |
| Franklin High | 604 | 583 |
| Cesar Chavez High | 603 | 604 |
| Stagg Senior High | 592 | 600 |
| Nightingale Elementary | 578 | 620 |
| Roosevelt Elementary | 578 | 593 |
| Edward C. Merlo Institute of Environmental Studies | 522 | 419 |
| Jane Frederick Continuation High | 416 | 329 |
| James Urbani Institute of Language Development | 415 | 431 |
| Moses Rodgers Virtual Learning Center | | |
| School for Adults | | |
| District Special Education | | |