| Skirball Cultural CenterEIN 95-4538371 | Arts, Culture, Humanities | CA | $25,294,003Large | 87.83 |
| 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 |
| Skylight Music TheatreEIN 39-0975374 | Arts, Culture, Humanities | WI | $3,499,182Small | 78.63 |
| 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 |
| SMARTEIN 93-1051724 | Education | OR | $3,497,122Small | 87.37 |
| Smith Center for Healing and the ArtsEIN 52-1977976 | Health | DC | $1,357,229Small | 89.35 |
| Smoky Hills Public TelevisionEIN 48-0874906 | Arts, Culture, Humanities | KS | $1,840,013Small | 79.50 |
| Smoky Mountain Children's HomeEIN 23-7110635 | Human Services | TN | $8,664,116Mid-sized | 87.30 |
| Smuin BalletEIN 94-3197247 | Arts, Culture, Humanities | CA | $4,135,237Mid-sized | 88.33 |
| 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 |
| Soaring EagleEIN 84-1409114 | Human Services | MT | $3,535,909Mid-sized | 79.67 |
| Social Venture PartnersEIN 91-1894424 | Research and Public Policy | WA | $2,722,955Small | 83.35 |
| 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 |
| Society for the Protection of New Hampshire ForestsEIN 02-0222237 | Environment | NH | $7,278,002Mid-sized | 94.94 |
| Society for Women's Health ResearchEIN 52-1694732 | Human and Civil Rights | DC | $1,749,602Small | 81.80 |
| Society of St. Vincent De Paul Archdiocesan Council of St. LouisEIN 43-0652684 | Human Services | MO | $23,619,507Large | 92.02 |
| Society of St. Vincent de Paul ChicagoEIN 36-3195567 | Human Services | IL | $4,872,627Mid-sized | 82.73 |
| Society of St. Vincent de Paul of Alameda CountyEIN 94-1156493 | Human Services | CA | $5,959,918Mid-sized | 84.57 |
| Society of St. Vincent de Paul of San Mateo CountyEIN 94-1375833 | Human Services | CA | $6,229,067Mid-sized | 87.77 |
| Society of St. Vincent de Paul, Portland CouncilEIN 93-0456525 | Human Services | OR | $7,058,723Mid-sized | 86.84 |
| Society of the CincinnatiEIN 53-0205423 | Arts, Culture, Humanities | DC | $4,196,909Mid-sized | 88.52 |
| Society of the Four ArtsEIN 59-0454318 | Arts, Culture, Humanities | FL | $8,133,941Mid-sized | 86.63 |
| Soil Born Farms Urban Agriculture & Education ProjectEIN 20-0774693 | Education | CA | $1,888,739Small | 79.87 |
| Sojourner CenterEIN 94-2465081 | Human Services | AZ | $7,335,341Mid-sized | 72.33 |
| Sojourner Family Peace CenterEIN 39-1276210 | Human Services | WI | $7,587,653Mid-sized | 83.73 |
| SojournersEIN 23-7380554 | Religion | DC | $5,042,915Mid-sized | 81.65 |
| Solar Cookers InternationalEIN 68-0153141 | Environment | CA | $773,030Small | 91.37 |
| Solar Electric Light FundEIN 52-1701564 | International | DC | $4,497,399Mid-sized | 89.02 |
| Soldiers' AngelsEIN 20-0583415 | Human Services | TX | $18,391,429Large | 94.28 |
| Soles4SoulsEIN 20-4023482 | International | TN | $83,106,075Large | 98.23 |
| Solid GroundEIN 36-3578158 | Human Services | MN | $1,371,215Small | 97.58 |
| Solid Rock InternationalEIN 34-1719319 | Religion | IN | $1,389,061Small | 96.88 |
| SoliyaEIN 32-0060209 | International | NY | $1,365,656Small | 72.22 |
| Solomon R. Guggenheim FoundationEIN 13-5562233 | Arts, Culture, Humanities | NY | $80,072,379Large | 78.32 |
| Solutions for ChangeEIN 33-0902617 | Human Services | CA | $3,329,200Small | 79.52 |
| SOLVEEIN 93-0579286 | Environment | OR | $1,209,987Small | 78.43 |
| Solve ME/CFS InitiativeEIN 56-1683450 | Health | CA | $1,925,767Small | 88.69 |
| SOMEEIN 23-7098123 | Human Services | DC | $28,344,473Large | 93.11 |
| Sonoma Valley Education FoundationEIN 68-0279152 | Education | CA | $1,722,094Small | 81.79 |
| Sonoran InstituteEIN 86-0684610 | Environment | AZ | $2,969,310Small | 82.94 |
| Sons of Italy FoundationEIN 23-6276526 | Community Development | DC | $991,230Small | 77.48 |
| SonScape RetreatsEIN 74-2372030 | Religion | CO | $1,005,888Small | 73.32 |
| SOS Children's Villages-USAEIN 13-6188433 | International | DC | $10,446,173Mid-sized | 77.68 |
| SOS International/SOS LocalEIN 87-0657642 | International | TX | $7,449,709Mid-sized | 88.68 |
| SoundWatersEIN 06-1263947 | Environment | CT | $2,007,465Small | 94.48 |
| South Africa Development FundEIN 22-2674813 | International | MA | $904,837Small | 78.60 |
| South Asian Youth ActionEIN 13-3943630 | Human Services | NY | $3,370,395Small | 95.04 |
| South Boston Neighborhood HouseEIN 04-2104807 | Human Services | MA | $1,756,067Small | 84.90 |
| South Carolina Governor's School for Science and Math FoundationEIN 57-0881347 | Education | SC | $2,340,649Small | 86.43 |
| South Carolina Woman's Missionary UnionEIN 57-0362065 | Religion | SC | $2,531,177Small | 79.42 |
| South Coast RepertoryEIN 95-6122708 | Arts, Culture, Humanities | CA | $11,651,004Mid-sized | 86.11 |
| South Coastal Counties Legal Services, Inc.EIN 04-3330208 | Human and Civil Rights | MA | $5,224,199Mid-sized | 87.14 |
| South Dakota Community FoundationEIN 46-0398115 | Community Development | SD | $13,502,997Large | 90.26 |