| San Francisco BalletEIN 94-1415298 | Arts, Culture, Humanities | CA | $50,771,268Large | 82.83 |
| San Francisco BaykeeperEIN 68-0120240 | Environment | CA | $1,512,332Small | 84.75 |
| San Francisco Museum of Modern ArtEIN 94-1156300 | Arts, Culture, Humanities | CA | $86,111,301Large | 85.61 |
| San Francisco OperaEIN 94-0836240 | Arts, Culture, Humanities | CA | $77,826,840Large | 87.05 |
| San Francisco PerformancesEIN 94-2600147 | Arts, Culture, Humanities | CA | $3,233,850Small | 88.79 |
| San Francisco ZooEIN 94-1429538 | Animals | CA | $24,928,934Large | 84.00 |
| San Jose Museum of ArtEIN 23-7062028 | Arts, Culture, Humanities | CA | $4,586,772Mid-sized | 89.14 |
| Sankara Nethralaya Om TrustEIN 52-1611548 | Health | MD | $912,982Small | 86.07 |
| Santa Barbara Bowl FoundationEIN 95-3618955 | Arts, Culture, Humanities | CA | $5,722,096Mid-sized | 89.24 |
| Santa Barbara Historical MuseumEIN 95-6005796 | Arts, Culture, Humanities | CA | $1,580,925Small | 85.57 |
| Santa Barbara Museum of Natural HistoryEIN 95-1643378 | Arts, Culture, Humanities | CA | $7,363,122Mid-sized | 88.67 |
| Santa Barbara Rescue MissionEIN 95-6134271 | Human Services | CA | $2,671,065Small | 83.81 |
| Santa Barbara Symphony Orchestra AssociationEIN 95-2104089 | Arts, Culture, Humanities | CA | $3,200,471Small | 87.97 |
| Santa Fe Art InstituteEIN 85-0404277 | Arts, Culture, Humanities | NM | $775,980Small | 83.63 |
| Santa Fe Chamber Music FestivalEIN 85-0224461 | Arts, Culture, Humanities | NM | $2,360,562Small | 82.12 |
| Santa Fe InstituteEIN 85-0325494 | Research and Public Policy | NM | $10,668,030Mid-sized | 84.43 |
| Sarasota OperaEIN 23-7089047 | Arts, Culture, Humanities | FL | $8,600,781Mid-sized | 86.80 |
| SAT-7EIN 23-2964829 | Religion | MD | $9,134,848Mid-sized | 82.79 |
| Savannah Music FestivalEIN 58-1401616 | Arts, Culture, Humanities | GA | $3,604,074Mid-sized | 85.71 |
| Save the ChildrenEIN 06-0726487 | International | CT | $719,647,258Large | 85.21 |
| Save the FamilyEIN 86-0665712 | Human Services | AZ | $5,414,265Mid-sized | 81.68 |
| Scholarship AmericaEIN 04-2296967 | Education | MN | $187,899,785Large | 86.07 |
| Scholarship Foundation of St. LouisEIN 43-6031234 | Education | MO | $6,200,105Mid-sized | 87.18 |
| Scholastic Art & Writing AwardsEIN 13-3780998 | Education | NY | $3,826,838Mid-sized | 81.28 |
| School for Advanced ResearchEIN 85-0125045 | Education | NM | $3,536,710Mid-sized | 88.22 |
| Schoolseed FoundationEIN 26-4477567 | Education | TN | $2,998,033Small | 88.14 |
| Science Center of IowaEIN 42-6097912 | Arts, Culture, Humanities | IA | $7,395,900Mid-sized | 88.53 |
| Science CentralEIN 31-1032583 | Arts, Culture, Humanities | IN | $1,724,835Small | 88.58 |
| Science Museum of MinnesotaEIN 41-0706172 | Arts, Culture, Humanities | MN | $39,667,153Large | 89.37 |
| Science Museum of Western VirginiaEIN 54-1023953 | Arts, Culture, Humanities | VA | $871,912Small | 88.97 |
| SCORE InternationalEIN 58-1605736 | Religion | TN | $8,470,138Mid-sized | 82.33 |
| Scottsdale Cultural CouncilEIN 86-0593786 | Arts, Culture, Humanities | AZ | $11,500,947Mid-sized | 82.14 |
| Scripture Union/USAEIN 25-1228715 | Religion | PA | $1,673,692Small | 83.74 |
| Sea Education AssociationEIN 04-2702102 | Education | MA | $8,416,413Mid-sized | 83.40 |
| SeaGate Food BankEIN 51-0252948 | Human Services | OH | $6,481,656Mid-sized | 88.83 |
| SeaShareEIN 91-1641242 | Human Services | WA | $3,409,125Small | 87.06 |
| 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 Audubon SocietyEIN 91-6009716 | Environment | WA | $1,068,105Small | 86.75 |
| Seattle Children's TheatreEIN 51-0172421 | Arts, Culture, Humanities | WA | $6,887,908Mid-sized | 86.49 |
| Seattle HumaneEIN 91-0282060 | Animals | WA | $6,703,024Mid-sized | 89.34 |
| 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 ChanceEIN 52-2276640 | Education | MD | $8,034,442Mid-sized | 85.43 |
| Second Harvest Food Bank of East Central IndianaEIN 31-1111795 | Human Services | IN | $14,490,604Large | 88.61 |
| Second Harvest Food Bank of Middle TennesseeEIN 62-1049447 | Human Services | TN | $86,355,168Large | 88.94 |
| Second Harvest HeartlandEIN 23-7417654 | Human Services | MN | $138,115,853Large | 85.05 |
| Second NatureEIN 04-3195772 | Environment | MA | $1,691,248Small | 89.82 |
| Seed Savers ExchangeEIN 43-1214133 | Environment | IA | $5,385,772Mid-sized | 84.73 |
| SEG FoundationEIN 73-1329755 | Education | OK | $2,969,212Small | 85.10 |
| 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 |
| Seneca Park Zoo SocietyEIN 16-0905390 | Animals | NY | $5,429,091Mid-sized | 81.24 |
| Senior ConcernsEIN 95-2992927 | Human Services | CA | $1,864,713Small | 84.52 |
| Senior Services Inc. of WichitaEIN 48-0757988 | Human Services | KS | $2,430,872Small | 86.19 |
| Service Over SelfEIN 62-1760415 | Human Services | TN | $1,554,211Small | 84.96 |
| SETI InstituteEIN 94-2951356 | Research and Public Policy | CA | $20,609,248Large | 87.01 |
| SFFILMEIN 94-2663216 | Arts, Culture, Humanities | CA | $6,042,427Mid-sized | 87.22 |
| SFJAZZEIN 94-2990335 | Arts, Culture, Humanities | CA | $16,924,582Large | 84.54 |
| Shake-A-Leg MiamiEIN 65-0611917 | Education | FL | $2,152,655Small | 83.20 |