| School Name | API |
| Commodore Stockton Skills | 802 |
| Rio Calaveras Elementary | 792 |
| Kohl Open Elementary | 768 |
| George W. Bush Elementary | 757 |
| Hazelton Elementary | 751 |
| Wilson Elementary | 750 |
| Maxine Hong Kingston Elementary | 741 |
| San Joaquin Elementary | 731 |
| Dolores Huerta Elementary | 731 |
| Valenzuela Elementary | 727 |
| Rosa Parks Academy | 726 |
| Victory Elementary | 722 |
| George Washington Elementary | 719 |
| Pulliam Elementary | 718 |
| John Marshall Elementary | 713 |
| Tyler Skills Elementary | 706 |
| Grunsky Elementary | 700 |
| Elmwood Elementary | 694 |
| Taft Elementary | 688 |
| El Dorado Elementary | 687 |
| Fillmore Elementary | 686 |
| Hoover Elementary | 685 |
| Monroe Elementary | 685 |
| McKinley Elementary | 682 |
| Madison Elementary | 674 |
| Adams Elementary | 671 |
| King Elementary | 670 |
| Harrison Elementary | 659 |
| Institute of Business, Management, and Law Charter | 656 |
| Weber Institute | 655 |
| Grant Elementary | 655 |
| Van Buren Elementary | 651 |
| Kennedy Elementary | 649 |
| Walton Development Center | 647 |
| Richard A. Pittman Elementary | 640 |
| Wilhelmina Henry Elementary | 638 |
| Taylor Skills Elementary | 638 |
| John C. Fremont Elementary | 635 |
| Cleveland Elementary | 633 |
| Montezuma Elementary | 624 |
| Cesar Chavez High | 611 |
| Stagg Senior High | 611 |
| Nightingale Elementary | 601 |
| Alexander Hamilton Elementary | 595 |
| Roosevelt Elementary | 586 |
| Edison High | 575 |
| Franklin High | 565 |
| Jane Frederick Continuation High | 360 |
| California Virtual Academy at San Joaquin | |
| Moses Rodgers Virtual Learning Center | |
| Valentine Peyton Elementary | |
| James Urbani Institute of Language Development | |
| Edward C. Merlo Institute of Environmental Studies | |
| School for Adults | |
| August Elementary | |
| District Special Education | |