| Scholarship AmericaEIN 04-2296967 | Education | MN | $187,899,785Large | 86.07 |
| Science Museum of MinnesotaEIN 41-0706172 | Arts, Culture, Humanities | MN | $39,667,153Large | 89.37 |
| Seattle Aquarium EIN 91-1189249 | Animals | WA | $16,757,036Large | 84.83 |
| Seattle Art MuseumEIN 91-0640788 | Arts, Culture, Humanities | WA | $38,076,158Large | 87.24 |
| Seattle FoundationEIN 91-6013536 | Community Development | WA | $110,286,703Large | 94.51 |
| Seattle OperaEIN 91-0760426 | Arts, Culture, Humanities | WA | $23,067,246Large | 82.88 |
| Seattle Repertory TheatreEIN 91-0756535 | Arts, Culture, Humanities | WA | $15,089,316Large | 84.81 |
| Second Harvest Food Bank of Central FloridaEIN 59-2142315 | Human Services | FL | $122,484,539Large | 92.92 |
| Second Harvest Food Bank of East Central IndianaEIN 31-1111795 | Human Services | IN | $14,490,604Large | 88.61 |
| Second Harvest Food Bank of East TennesseeEIN 58-1450139 | Human Services | TN | $29,394,281Large | 90.23 |
| Second Harvest Food Bank of Greater New Orleans and AcadianaEIN 72-0956468 | Human Services | LA | $73,953,206Large | 94.69 |
| Second Harvest Food Bank of MetrolinaEIN 56-1352593 | Human Services | NC | $97,534,285Large | 90.22 |
| Second Harvest Food Bank of Middle TennesseeEIN 62-1049447 | Human Services | TN | $86,355,168Large | 88.94 |
| Second Harvest Food Bank of Northeast TennesseeEIN 62-1303822 | Human Services | TN | $20,333,455Large | 93.56 |
| Second Harvest Food Bank of Northwest North CarolinaEIN 58-1457912 | Human Services | NC | $60,851,278Large | 96.46 |
| Second Harvest Food Bank of Northwest PennsylvaniaEIN 25-1405798 | Human Services | PA | $18,759,837Large | 92.92 |
| 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 HeartlandEIN 23-7417654 | Human Services | MN | $138,115,853Large | 85.05 |
| Second Harvest Inland NorthwestEIN 23-7173826 | Human Services | WA | $104,702,103Large | 93.32 |
| Segerstrom Center for the ArtsEIN 23-7287150 | Arts, Culture, Humanities | CA | $69,295,404Large | 89.82 |
| Self Enhancement, Inc.EIN 93-1086629 | Human Services | OR | $16,850,558Large | 86.57 |
| SergeEIN 23-2223692 | Religion | PA | $14,401,712Large | 96.81 |
| SeriousFun Children's NetworkEIN 31-1794455 | Health | CT | $14,274,438Large | 91.85 |
| SETI InstituteEIN 94-2951356 | Research and Public Policy | CA | $20,609,248Large | 87.01 |
| SFJAZZEIN 94-2990335 | Arts, Culture, Humanities | CA | $16,924,582Large | 84.54 |
| Shakespeare Theatre CompanyEIN 52-1405988 | Arts, Culture, Humanities | DC | $21,930,518Large | 87.67 |
| Shalom AustinEIN 74-1469465 | Human Services | TX | $13,606,228Large | 85.00 |
| Share Our SelvesEIN 95-3222316 | Human Services | CA | $17,655,264Large | 90.63 |
| Share Our StrengthEIN 52-1367538 | Human Services | DC | $51,056,766Large | 80.07 |
| Shedd AquariumEIN 36-2167918 | Animals | IL | $59,336,621Large | 90.86 |
| Sheltering Arms Early Education & Family CentersEIN 58-0566236 | Education | GA | $30,964,764Large | 89.87 |
| Shriners Hospitals for ChildrenEIN 36-2193608 | Health | FL | $856,243,943Large | 95.61 |
| Sierra Club FoundationEIN 94-6069890 | Environment | CA | $72,890,348Large | 95.21 |
| Single Stop USAEIN 20-8837690 | Human Services | NY | $21,924,829Large | 80.68 |
| Skid Row Housing TrustEIN 95-4205316 | Community Development | CA | $21,003,687Large | 81.70 |
| 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 |
| Society for Science & the PublicEIN 53-0196483 | Education | DC | $28,626,131Large | 97.23 |
| Society of St. Vincent De Paul Archdiocesan Council of St. LouisEIN 43-0652684 | Human Services | MO | $23,619,507Large | 92.02 |
| Soldiers' AngelsEIN 20-0583415 | Human Services | TX | $18,391,429Large | 94.28 |
| Soles4SoulsEIN 20-4023482 | International | TN | $83,106,075Large | 98.23 |
| Solomon R. Guggenheim FoundationEIN 13-5562233 | Arts, Culture, Humanities | NY | $80,072,379Large | 78.32 |
| SOMEEIN 23-7098123 | Human Services | DC | $28,344,473Large | 93.11 |
| South Dakota Community FoundationEIN 46-0398115 | Community Development | SD | $13,502,997Large | 90.26 |
| South Florida PBSEIN 59-0737868 | Arts, Culture, Humanities | FL | $18,553,742Large | 78.65 |
| South Plains Food BankEIN 75-1904829 | Human Services | TX | $15,594,953Large | 90.67 |
| Southeast Missouri Food BankEIN 43-1395863 | Human Services | MO | $16,120,107Large | 97.17 |
| Southern California Public RadioEIN 95-4765734 | Arts, Culture, Humanities | CA | $27,593,781Large | 85.94 |
| Southern Environmental Law CenterEIN 52-1436778 | Environment | VA | $26,551,471Large | 100.00 |
| Southern Poverty Law CenterEIN 63-0598743 | Human and Civil Rights | AL | $59,784,321Large | 88.78 |
| SPCA InternationalEIN 87-0773320 | Animals | NY | $14,673,812Large | 72.62 |
| SPCA of TexasEIN 75-1216660 | Animals | TX | $18,553,754Large | 95.77 |
| Special OlympicsEIN 52-0889518 | Human Services | DC | $110,965,732Large | 90.49 |
| Special Olympics FloridaEIN 23-7181560 | Human Services | FL | $13,729,105Large | 92.61 |
| Sponsors for Educational Opportunity (SEO)EIN 13-2578670 | Education | NY | $17,839,508Large | 99.93 |
| St. Anne'sEIN 95-1691306 | Human Services | CA | $25,417,077Large | 93.91 |