| OMAHA ZOOLOGICAL SOCIETY | Omaha | D500 Animal-Related | $82M | 10 |
| FIRST NATIONAL OF NEBRASKA INC WELFARE | Omaha | Y43 Mutual & Membership Benefit | $76.8M | 1 |
| NEBRASKA HEART HOSPITAL | Lincoln | — | $76.7M | 13 |
| CONCORDIA UNIVERSITY | Seward | B500 Education | $74.3M | 5 |
| ONEWORLD COMMUNITY HEALTH CENTERS INC | Omaha | — | $73.9M | 9 |
| FOUNDATION FOR AFFORDABLE HOUSING | Omaha | L200 Housing & Shelter | $72.6M | 6 |
| Grand Island Regional Medical Center Inc | Grand Island | E20 Health Care | $67.8M | 12 |
| NEBRASKA COMMUNITY FOUNDATION | Lincoln | T31 Philanthropy, Voluntarism & Grantmaking Foundations | $66.5M | 8 |
| FOOD BANK FOR THE HEARTLAND | Omaha | — | $66M | 3 |
| YORK GENERAL HEALTH CARE SERVICES | York | E220 Health Care | $65.9M | 13 |
| CHILDREN'S PHYSICIANS | Omaha | E32Z Health Care | $65.1M | 6 |
| DOANE UNIVERSITY | Crete | B420 Education | $63.1M | 11 |
| Nebraska Medicine | Omaha | E21 Health Care | $63M | 4 |
| MIDLAND UNIVERSITY | Fremont | B420 Education | $62.3M | 8 |
| William and Ruth Scott Family Foundation | Omaha | T99 Philanthropy, Voluntarism & Grantmaking Foundations | $61.2M | 1 |
| COMMUNITY HOSPITAL ASSOCIATION OF MCCOOK | McCook | E22Z Health Care | $60M | 7 |
| IMMANUEL | Omaha | E210 Health Care | $59.5M | 9 |
| REGIONAL WEST PHYSICIANS CLINIC | Scottsbluff | X99Z Religion-Related | $58.7M | 27 |
| FRANCISCAN CARE SERVICES INC | West Point | E22 Health Care | $55.5M | 10 |
| HASTINGS COLLEGE | Hastings | B420 Education | $54.3M | 4 |
| MEMORIAL COMMUNITY HOSPITAL | Blair | E21Z Health Care | $54.1M | 7 |
| ORPHAN GRAIN TRAIN INC | Norfolk | Q330 International, Foreign Affairs & National Security | $53.7M | 1 |
| THE LOZIER FOUNDATION | Omaha | T20 Philanthropy, Voluntarism & Grantmaking Foundations | $50.6M | 1 |
| IMMANUEL RETIREMENT COMMUNITIES INC | Omaha | L220 Housing & Shelter | $49.7M | 9 |
| INCEPTIA | Lincoln | B82 Education | $47.7M | 12 |
| MEMORIAL HEALTH CARE SYSTEMS | Seward | E22Z Health Care | $47.1M | 7 |
| Avera St Anthony's Hospital | Oneill | E22 Health Care | $46.7M | 9 |
| PACE IOWA | Omaha | E19 Health Care | $46.4M | 9 |
| Omaha Community Foundation | Omaha | T31 Philanthropy, Voluntarism & Grantmaking Foundations | $44.7M | 7 |
| NEBRASKA CHILDREN & FAMILIES FOUNDATION | Lincoln | T70 Philanthropy, Voluntarism & Grantmaking Foundations | $44.1M | 9 |
| ST MARY'S COMMUNITY HOSPITAL | Nebraska City | E220 Health Care | $42.5M | 14 |
| Tabitha Inc | Lincoln | — | $42.3M | 0 |
| BRODSTONE MEMORIAL HOSPITAL | Superior | E22Z Health Care | $42.2M | 7 |
| Lincoln Community Foundation Inc | Lincoln | T310 Philanthropy, Voluntarism & Grantmaking Foundations | $38.4M | 4 |
| DELTA DENTAL OF NEBRASKA | Omaha | — | $38.4M | 11 |
| COMMUNITY MEDICAL CENTER INC | Falls City | E020 Health Care | $38.2M | 8 |
| HABITAT FOR HUMANITY OF OMAHA INC | Omaha | L200 Housing & Shelter | $38.2M | 7 |
| IBEW LOCAL UNION NO 22NECA | Omaha | — | $37.6M | 0 |
| Clarkson College | Omaha | — | $37.5M | 7 |
| LUTHERAN FAMILY SERVICES OF NE INC | Omaha | P40 Human Services | $37.4M | 6 |
| LIBERTY FIRST CREDIT UNION | Lincoln | — | $37M | 11 |
| ROBERT B DAUGHERTY FOUNDATION | Omaha | — | $36.7M | 8 |
| JEWISH FEDERATION OF OMAHA INC | Omaha | T700 Philanthropy, Voluntarism & Grantmaking Foundations | $36.6M | 8 |
| Crete Area Medical Center | Crete | E22 Health Care | $35.9M | 10 |
| JEFFERSON COMMUNITY HEALTH CENTER INC | Fairbury | E22 Health Care | $35.7M | 7 |
| QUALITY LIVING INC | Omaha | E500 Health Care | $35.2M | 9 |
| HEARTLAND FAMILY SERVICE | Omaha | P40Z Human Services | $34.7M | 7 |
| GOODWILL INDUSTRIES INC | Omaha | J32Z Employment | $33.9M | 6 |
| BUFFETT EARLY CHILDHOOD FUND | Omaha | T20 Philanthropy, Voluntarism & Grantmaking Foundations | $33.7M | 2 |
| CHADRON COMMUNITY HOSPITAL CORPORATION | Chadron | — | $32.2M | 7 |
