| University of the Pacific | 501(c)(3) | 1963 | $588 million | $1.56 billion | 2025-06 |
| Able Charter Schools | 501(c)(3) | 2013 | $22.4 million | $38 million | 2025-06 |
| Transformational Education Inc | 501(c)(3) | 2012 | $16.4 million | $26.1 million | 2025-06 |
| Stockton Collegiate International Schools | 501(c)(3) | 2010 | $14.1 million | $49.1 million | 2025-06 |
| Humphreys College | 501(c)(3) | 1948 | $11.8 million | $32.7 million | 2025-06 |
| Dr Lewis Dolphin Stallworth Sr Charter School Inc | 501(c)(3) | 2025 | $5.7 million | $6.2 million | 2025-06 |
| El Concilio California Academies | 501(c)(3) | 2022 | $4.6 million | $3.3 million | 2025-06 |
| San Joaquin A Plus Inc | 501(c)(3) | 2007 | $2.5 million | $9.4 million | 2024-12 |
| San Joaquin & Calaveras Co Electric Training & Educational Trust | 501(c)(3) | 2007 | $2.1 million | $5.8 million | 2025-12 |
| A Tavola Together Foundation | 501(c)(3) | 2008 | $1.9 million | $969,036 | 2024-12 |
| Friends of the Children - Stockton | 501(c)(3) | 2024 | $1.7 million | $1.4 million | 2025-08 |
| Brookside Christian School Inc | 501(c)(3) | 1987 | $1.5 million | $3.8 million | 2025-07 |
| California Coalition of Early & Middle Colleges | 501(c)(3) | 2017 | $1.2 million | $1.1 million | 2025-06 |
| Harvest Preschool and Child Care | 501(c)(3) | 2018 | $371,582 | $160,749 | 2025-12 |
| San Joaquin County Office of Education Educational Foundation | 501(c)(3) | 1995 | $328,568 | $1.1 million | 2025-06 |
| Escuchen Mi Voz | 501(c)(3) | 2024 | $292,916 | $68,687 | 2025-06 |
| Andhra Medical College of North America | 501(c)(3) | 2005 | $220,497 | $1 million | 2024-12 |
| Angel S Recovery Dive Team Inc | 501(c)(3) | 2024 | $193,576 | $175,849 | 2025-12 |
| Alpha Psi Education Scholarship and Leadership Foundation Inc | 501(c)(3) | 2008 | $192,226 | $1.3 million | 2025-12 |
| Northern California Band Association Inc | 501(c)(3) | 2017 | $124,597 | $61,662 | 2025-06 |
| Library Literacy Foundation of San Joaquin County | 501(c)(3) | 1996 | $113,143 | $2.1 million | 2025-06 |
| TLC Foundation for Homeless Children of San Joaquin County | 501(c)(3) | 2010 | $90,737 | $718,211 | 2025-12 |
| San Joaquin County Housing Authority Scholarship Foundation I | 501(c)(3) | 2009 | $81,968 | $662,893 | 2025-12 |
| Leadership Stockton Alumni Association | 501(c)(3) | 1998 | $78,194 | $40,220 | 2026-06 |
| Gigamind Explorer Education | 501(c)(3) | 2015 | $59,688 | $237,707 | 2025-12 |
| Yaqui Lopezs Fat City Boxing Gym | 501(c)(3) | 2017 | $53,010 | $28,650 | 2025-12 |
| Aauw Stockton Branch Community Outreach Fund Inc | 501(c)(3) | 1999 | $52,923 | $93,123 | 2026-06 |
| Future Education Initiative Inc | 501(c)(3) | 2021 | $49,553 | $100,622 | 2024-12 |
| American Council of Teachers Inc | 501(c)(3) | 2017 | $45,555 | $3,630 | 2024-12 |
| A A Stagg High Athletic Booster Club Inc | 501(c)(3) | 2002 | $43,935 | $81,699 | 2025-06 |
| Friends of Walton Booster Club | 501(c)(3) | 1997 | $40,891 | $58,596 | 2025-05 |
| Kohl Educational Foundation | 501(c)(3) | 2010 | $39,437 | $117,876 | 2024-12 |
| Lincoln High School Grad Night | 501(c)(3) | 1998 | $24,307 | $24,895 | 2025-09 |
| New Toyz Association | 501(c)(3) | 2023 | $14,530 | $1 | 2024-12 |
| Stockton Unified School District 1852 Foundation | 501(c)(3) | 2025 | $8,787 | $129,314 | 2025-06 |
| Ankineedu Foundation Inc | 501(c)(3) | 2020 | $8,500 | $1,685 | 2024-12 |
| Waverly PTC | 501(c)(3) | 2013 | $6,070 | $14,152 | 2025-06 |
| The Pacific Alumni House Board of Sigma Chi | 501(c)(7) | 2007 | $1 | $27,361 | 2025-06 |
| 32elite | 501(c)(3) | 2024 | | | |
| A A Stagg Alumni Association | 501(c)(3) | 2014 | $0 | $0 | 2025-06 |
| Alex and Faye Spanos Family Foundation | 501(c)(3) | 1998 | | $1 | 2024-12 |
| Alpha Psi Chapter of Phi Delta Chi Pharmacy Fraternity | 501(c)(7) | 2016 | $0 | $0 | 2025-07 |
| American Pakistani Association of San Joaquin County | 501(c)(3) | 2017 | | $664 | 2025-12 |
| Andronicus Alumni Association | 501(c)(3) | 2025 | | | |
| BW Foundation Inc | 501(c)(3) | 2014 | | $1.2 million | 2025-12 |
| Bear Creek High School Friends of Music | 501(c)(3) | 2005 | $0 | $0 | 2025-12 |
| Bridge the Gap Young Adult Support Inc | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Central Valley Feat | 501(c)(3) | 1997 | $0 | $0 | 2026-02 |
| Cesar Chavez High School Band Boosters Inc | 501(c)(3) | 2008 | $0 | $0 | 2025-06 |
| Chicano Research Center | 501(c)(3) | 2016 | | $113,878 | 2024-12 |
| Choices Institute | 501(c)(3) | 2022 | $0 | $0 | 2024-06 |
| Combat Veterans of America Association Inc | 501(c)(3) | 2022 | $0 | $3,766 | 2025-12 |
| Cyrilla Olapeju Sanni Scholarship Fund | 501(c)(3) | 2021 | $0 | $0 | 2025-12 |
| Dave Mendoza Scholarship Fund | 501(c)(3) | 2024 | | | |
| David P Jackson Memorial Foundation | 501(c)(3) | 2009 | $0 | $0 | 2025-12 |
| Davis Elementary Parent Teacher Organization | 501(c)(3) | 2025 | | | |
| Diamond Cove Housing Corporation | 501(c)(3) | 1996 | $0 | $0 | 2025-12 |
| Edison Alumni Association of Stockton Ca | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |
| Education Empowerment Action | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Eleanor P Touhey Schlorship Fund Trust | 501(c)(3) | 1999 | | $279,126 | 2024-12 |
| Elkhorn Pto | 501(c)(3) | 2025 | $0 | $0 | 2026-06 |
| Empoweryou University | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| Esquire Club Inc | 501(c)(3) | 2008 | $0 | $0 | 2024-12 |
| First Baptist Christian Schools of Stockton California | 501(c)(3) | 2006 | | | |
| Franklin International Baccalaureate Booster Club | 501(c)(3) | 2003 | $0 | $0 | 2024-05 |
| Friends of CMMS Music | 501(c)(3) | 2022 | $0 | $0 | 2025-07 |
| Friends of Young Adult Program Boosters | 501(c)(3) | 2022 | $0 | $0 | 2025-12 |
| Godwin Ogbeide Scholarship Foundati On | 501(c)(3) | 2026 | | | |
| Green & White Foundation Inc | 501(c)(3) | 2009 | $0 | $0 | 2025-12 |
| HB Dhanda Foundation | 501(c)(3) | 2021 | $0 | $0 | 2025-12 |
| Hazelton A C T Team Booster Club | 501(c)(3) | 1999 | $0 | $0 | 2025-06 |
| Honor Society of Phi Kappa Phi | 501(c)(3) | 1999 | $0 | $0 | 2026-06 |
| Institute for Western Maritime Archaeology | 501(c)(3) | 2012 | $0 | $0 | 2025-12 |
| Kalimah Learning & Tutoring | 501(c)(3) | 2026 | | | |
| Kamcosa Inc | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| Kappa Psi Gamma Nu Education Foundation | 501(c)(3) | 2012 | $0 | $0 | 2025-06 |
| King Family Center Parent Association | 501(c)(3) | 2014 | $0 | $0 | 2025-12 |
| Lincoln High School Alumni Association | 501(c)(3) | 2018 | $0 | $0 | 2025-06 |
| Make Every Move Count Inc | 501(c)(3) | 2022 | $0 | $0 | 2025-09 |
| Miri Piri Educational Society | 501(c)(3) | 2026 | | | |
| Monica Deangelo Scholarship-Foundat Ion | 501(c)(3) | 2026 | | | |
| Mosher Club | 501(c)(3) | 2025 | | | |
| Nak Delta Chapter Scholarship Foundation | 501(c)(3) | 2021 | $0 | $0 | 2023-12 |
| New Nankai Foundation Inc | 501(c)(3) | 2019 | | $4,971 | 2025-06 |
| Oak Park Junior Tennis Foundation | 501(c)(3) | 2003 | $0 | $0 | 2025-12 |
| Ole Soccer Academy | 501(c)(3) | 2019 | | $8,714 | 2025-12 |
| Open Innovation Centers | 501(c)(3) | 2024 | $0 | $0 | 2024-12 |
| Pacific Swimming and Waterpolo Foundation | 501(c)(3) | 1999 | $0 | $0 | 2025-12 |
| Parent Booster USA Inc | 501(c)(3) | 2005 | $0 | $0 | 2025-06 |
| Past Due Connections | 501(c)(3) | 2026 | $0 | $0 | 2025-09 |
| People for Academic and Social Chan Ge Pasc | 501(c)(3) | 2024 | $0 | $0 | 2026-07 |
| Peripheral Arterial Disease & Amput Ee Support Group of Stockton Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Pi Kappa Alpha Kappa Nu | 501(c)(7) | 1941 | $0 | $0 | 2023-12 |
| Progressive Community Church of Stockton | 501(c)(3) | 1995 | | | 2013-12 |
| Real Help Inc | 501(c)(3) | 2025 | $0 | $0 | 2025-12 |
| Richfriend Foundation | 501(c)(3) | 2024 | $0 | $0 | 2025-12 |
| River Oaks Charter Council Pto | 501(c)(3) | 2024 | | | |
| Ryandas Legacy Foundation | 501(c)(3) | 2023 | $0 | $0 | 2025-12 |
| San Joaquin Delta College Nursing Alumni Association | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| San Joaquin Pto | 501(c)(3) | 2014 | $0 | $0 | 2025-06 |
| Scholarship Foundation of San Joaquin Division 20 | 501(c)(3) | 1994 | $0 | $0 | 2024-06 |
| Sjcdsa Charitable Trust Fund | 501(c)(3) | 1996 | | $911,264 | 2025-12 |
| Spanos Education Foundation Inc | 501(c)(3) | 2019 | $0 | $0 | 2025-12 |
| Stockton Lapidary & Mineral Club | 501(c)(3) | 1996 | $0 | $0 | 2025-12 |
| Stockton Mexican Athletic Scholarship Committee | 501(c)(3) | 2010 | $0 | $0 | 2025-09 |
| Sutherland School Parent Teacher Organization | 501(c)(3) | 2023 | $0 | $0 | 2026-06 |
| The Azul Marine Group | 501(c)(3) | 2026 | | | |
| Transition U | 501(c)(3) | 2020 | $0 | $0 | 2025-12 |
| United All the Way | 501(c)(3) | 2026 | $0 | $0 | 2025-12 |
| Uwazi Foundation International | 501(c)(3) | 2025 | | | |
| Van Lang Vietnamese Language School | 501(c)(3) | 2022 | $0 | $0 | 2025-12 |
| WLC Family Foundation | 501(c)(3) | 2015 | | $953,116 | 2025-10 |
| West Coast Carriers Foundation | 501(c)(3) | 2019 | | $307,584 | 2025-12 |
| Weston Ranch High School Band & Boosters Inc | 501(c)(3) | 2018 | $0 | $0 | 2023-12 |
| Women of Color International Stockton | 501(c)(3) | 2015 | $0 | $0 | 2025-12 |