| MARTY INDIAN SCHOOL BOARD INC | Marty | B20Z Education | $8.3M | 0 |
| Clay Rural Water System Inc | Wakonda | — | $8.2M | 10 |
| CRAZY HORSE SCHOOL | Wanblee | B24Z Education | $8.2M | 9 |
| INDIAN BOARD OF EDUCATION FOR THE | Pierre | P620 Human Services | $8M | 17 |
| MINNEHAHA COMMUNITY WATER CORP | Dell Rapids | — | $8M | 8 |
| WAITT INSTITUTE | North Sioux City | A05 Arts, Culture & Humanities | $7.9M | 1 |
| EAST DAKOTA EDUCATIONAL COOPERATIVE | Sioux Falls | — | $7.8M | 2 |
| MOREAU GRAND ELECTRIC COOPERATIVE | Timber Lake | — | $7.7M | 14 |
| South Lincoln Rural Water System Inc | Beresford | — | $7.7M | 8 |
| Sesdac Inc | Vermillion | F330 Mental Health & Crisis Intervention | $7.6M | 0 |
| CAPITAL AREA COUNSELING SERVICEINC | Pierre | F32Z Mental Health & Crisis Intervention | $7.6M | 1 |
| NORTHERN HILLS TRAINING CENTER INC | Spearfish | J30Z Employment | $7.5M | 1 |
| Brookings Deuel Rural Water System | Toronto | — | $7.5M | 9 |
| BOYS & GIRLS CLUB | Brookings | O23 Youth Development | $7.4M | 5 |
| HARVEY W PETERS RESEARCH FOUNDATION | Sioux Falls | H99 Medical Research | $7.3M | 0 |
| United Retirement Center | Brookings | P700 Human Services | $7.2M | 1 |
| TIESZEN MEMORIAL HOME | Marion | Z99Z Unknown | $7.2M | 9 |
| DAKOTA COUNSELING INSTITUTE INC | Mitchell | F30Z Mental Health & Crisis Intervention | $7M | 1 |
| SOUTH DAKOTA LIONS EYE AND TISSUE | Sioux Falls | E99Z Health Care | $7M | 1 |
| SOUTH DAKOTA URBAN INDIAN HEALTH INC | Sioux Falls | — | $7M | 2 |
| Enemy Swim Day School | Waubay | — | $6.9M | 7 |
| LANDMANN-JUNGMAN MEMORIAL HOSPITAL | Scotland | E22 Health Care | $6.9M | 5 |
| YELLOW JACKET FOUNDATION | Spearfish | — | $6.9M | 1 |
| LAKE AREA IMPROVEMENT CORPORATION | Madison | S30Z Community Improvement & Capacity Building | $6.9M | 1 |
| THUNDER VALLEY COMMUNITY DEVELOPMENT COR | Porcupine | S20 Community Improvement & Capacity Building | $6.7M | 8 |
| BETHEL LUTHERAN HOME | Madison | P750 Human Services | $6.7M | 1 |
| Northeastern Mental Health Center | Aberdeen | F32Z Mental Health & Crisis Intervention | $6.6M | 2 |
| LONEMAN SCHOOL CORPORATION | Oglala | B24I Education | $6.5M | 3 |
| The Carroll Institute | Sioux Falls | F34Z Mental Health & Crisis Intervention | $6.5M | 2 |
| Aberdeen Family YMCA | Aberdeen | — | $6.4M | 2 |
| WEST RIVER LYMAN JONES RURAL WATER | Murdo | — | $6.3M | 12 |
| Honor the Earth | Rapid City | C30 Environment | $6.2M | 1 |
| SOUTH DAKOTA LIFE AND HEALTH INSURANCE | Sioux Falls | — | $6.1M | 0 |
| CORNERSTONE RESCUE MISSION | Rapid City | — | $6.1M | 1 |
| THE EVANGELICAL LUTHERAN GOOD SAMARITAN | Sioux Falls | X20 Religion-Related | $6M | 5 |
| COMMUNITY COUNSELING SERVICES | Huron | — | $6M | 4 |
| HELPLINE CENTER INC | Sioux Falls | — | $5.9M | 1 |
| THE LUKE SOCIETY INC | Sioux Falls | — | $5.9M | 3 |
| LIFESCAPE FOUNDATION | Sioux Falls | E50J Health Care | $5.8M | 3 |
| EUREKA COMMUNITY BENEVOLENT | Eureka | E22 Health Care | $5.8M | 4 |
| VALIANT LIVING INCORPORATED | Madison | J330 Employment | $5.7M | 2 |
| AKIPTAN INC | Eagle Butte | W60 Public & Societal Benefit | $5.7M | 1 |
| SUNSET MANOR INC | Irene | E91Z Health Care | $5.6M | 1 |
| BETHESDA OF BERESFORD | Beresford | — | $5.6M | 1 |
| Grant-Roberts Rural Water System Inc | Milbank | — | $5.5M | 8 |
| BLACK HILLS EDUCATIONAL INSTITUTE INC | Rapid City | B64Z Education | $5.5M | 0 |
| BETHESDA HOME INC | Webster | — | $5.4M | 0 |
| ESTHER AND HAROLD MERTZ FOUNDATION | Sioux Falls | T22 Philanthropy, Voluntarism & Grantmaking Foundations | $5.4M | 2 |
| WESTERN SOUTH DAKOTA COMMUNITY | Rapid City | S20Z Community Improvement & Capacity Building | $5.4M | 1 |
| ST WILLIAM'S CARE CENTER | Milbank | — | $5.4M | 2 |
