| Second Harvest Food Bank of Orange CountyEIN 32-0362611 | Human Services | CA | $53,968,186Large | 96.80 |
| Second Harvest Food Bank of Santa Clara and San Mateo CountiesEIN 94-2614101 | Human Services | CA | $125,127,781Large | 97.68 |
| Second Harvest Food Bank Santa Cruz CountyEIN 77-0326685 | Human Services | CA | $19,193,561Large | 92.74 |
| Second Harvest Foodbank of Southern WisconsinEIN 39-1490691 | Human Services | WI | $33,052,619Large | 96.55 |
| Second Harvest Foodbank of the Mahoning ValleyEIN 34-1380074 | Human Services | OH | $17,272,324Large | 98.06 |
| Second Harvest Inland NorthwestEIN 23-7173826 | Human Services | WA | $104,702,103Large | 93.32 |
| Second Harvest Northern Lakes Food BankEIN 36-3479964 | Human Services | MN | $10,915,737Mid-sized | 94.46 |
| Second HelpingsEIN 35-1484281 | Human Services | IN | $6,711,056Mid-sized | 98.23 |
| Second StoryEIN 54-0899463 | Human Services | VA | $3,085,749Small | 91.02 |
| Sedgwick County Zoological SocietyEIN 48-6120530 | Animals | KS | $11,658,916Mid-sized | 90.32 |
| Seeds of Hope Charitable TrustEIN 84-1437053 | Education | CO | $2,367,910Small | 100.00 |
| Senator John Heinz History Center- Historical Society of Western PennsylvaniaEIN 25-0965391 | Arts, Culture, Humanities | PA | $11,115,252Mid-sized | 90.62 |
| Senior Link MidlandEIN 75-1899190 | Human Services | TX | $2,885,630Small | 90.74 |
| Senior NeighborsEIN 23-7195491 | Human Services | MI | $3,594,979Mid-sized | 94.69 |
| Senior ServicesEIN 56-1085968 | Human Services | NC | $6,935,007Mid-sized | 95.38 |
| SergeEIN 23-2223692 | Religion | PA | $14,401,712Large | 96.81 |
| SeriousFun Children's NetworkEIN 31-1794455 | Health | CT | $14,274,438Large | 91.85 |
| Settlement Music SchoolEIN 23-1352676 | Education | PA | $10,681,642Mid-sized | 90.42 |
| Seva FoundationEIN 38-2231279 | International | CA | $7,518,689Mid-sized | 92.27 |
| Several Sources SheltersEIN 22-2368937 | Human Services | NJ | $2,363,897Small | 93.65 |
| Sewa International, IncEIN 20-0638718 | International | TX | $2,137,807Small | 100.00 |
| Sexual Assault CenterEIN 62-1043294 | Human Services | TN | $2,597,107Small | 91.17 |
| SHAREEIN 13-3131914 | Health | NY | $1,754,882Small | 91.66 |
| Share & Care FoundationEIN 22-2458395 | International | NJ | $1,801,384Small | 94.79 |
| Share Our SelvesEIN 95-3222316 | Human Services | CA | $17,655,264Large | 90.63 |
| Shared Hope InternationalEIN 91-1938635 | International | WA | $3,062,526Small | 90.90 |
| Sharing ConnectionsEIN 36-4363123 | Human Services | IL | $2,816,731Small | 90.62 |
| SharsheretEIN 13-4198529 | Health | NJ | $2,330,300Small | 99.43 |
| Shedd AquariumEIN 36-2167918 | Animals | IL | $59,336,621Large | 90.86 |
| Sheffield PlaceEIN 43-1532267 | Human Services | MO | $1,187,546Small | 100.00 |
| Shelburne FarmsEIN 03-0229347 | Environment | VT | $5,255,194Mid-sized | 91.56 |
| Shelby County United WayEIN 34-4473288 | Community Development | OH | $1,440,609Small | 92.66 |
| Shelter PartnershipEIN 95-3976214 | Human Services | CA | $11,932,800Mid-sized | 93.29 |
| ShelterBox USAEIN 20-0471604 | International | FL | $5,478,172Mid-sized | 94.42 |
| Sheltering Wings Center for WomenEIN 35-2077713 | Human Services | IN | $1,678,269Small | 92.18 |
| Shepherd Community CenterEIN 35-1765846 | Human Services | IN | $6,208,023Mid-sized | 90.47 |
| Sheridan House Family MinistriesEIN 59-1258384 | Human Services | FL | $4,200,026Mid-sized | 90.19 |
| Sherwood Forest CampEIN 43-0653401 | Human Services | MO | $1,738,056Small | 94.76 |
| Shoes and Clothes for KidsEIN 34-1554285 | Human Services | OH | $5,419,032Mid-sized | 97.17 |
| Shoes That FitEIN 95-4425565 | Human Services | CA | $5,130,693Mid-sized | 94.69 |
| Shoreline Soup Kitchens & PantriesEIN 46-3773017 | Human Services | CT | $1,555,411Small | 93.84 |
| Shriners Hospitals for ChildrenEIN 36-2193608 | Health | FL | $856,243,943Large | 95.61 |
| Siena/Francis HouseEIN 47-0601005 | Human Services | NE | $8,429,303Mid-sized | 97.03 |
| Sierra Club FoundationEIN 94-6069890 | Environment | CA | $72,890,348Large | 95.21 |
| Sightline InstituteEIN 52-1833599 | Research and Public Policy | WA | $1,600,591Small | 91.66 |
| SIGN Fracture Care InternationalEIN 91-1952283 | International | WA | $5,661,218Mid-sized | 94.39 |
| Sioux Empire United WayEIN 46-0233701 | Community Development | SD | $9,634,756Mid-sized | 92.22 |
| Sister Carmen Community CenterEIN 84-0820308 | Human Services | CO | $4,207,307Mid-sized | 90.32 |
| Skin Cancer FoundationEIN 13-2948778 | Health | NY | $4,550,855Mid-sized | 92.38 |
| SKY Family YMCAEIN 59-1629660 | Human Services | FL | $14,895,916Large | 91.77 |
| Sky Island AllianceEIN 86-0796748 | Environment | AZ | $1,171,111Small | 97.70 |
| Slavic Village DevelopmentEIN 34-1344279 | Community Development | OH | $2,669,057Small | 92.24 |
| Small Steps Nurturing CenterEIN 76-0471755 | Education | TX | $3,461,219Small | 91.82 |
| SMVA TrustEIN 23-2785411 | International | TX | $1,015,991Small | 92.22 |
| Snow Leopard TrustEIN 91-1144119 | Animals | WA | $2,389,563Small | 93.73 |
| SnowCap Community CharitiesEIN 23-7121915 | Human Services | OR | $4,003,598Mid-sized | 96.53 |
| Sociedad LatinaEIN 04-2678255 | Human Services | MA | $1,814,005Small | 93.02 |
| Society for Classical StudiesEIN 13-6018127 | Education | NY | $1,277,954Small | 93.82 |
| Society for Science & the PublicEIN 53-0196483 | Education | DC | $28,626,131Large | 97.23 |
| Society for the Improvement of Conditions for Stray AnimalsEIN 23-7367199 | Animals | OH | $1,504,640Small | 95.60 |