| Concordia Jr.-Sr. High School | Omaha | K-12 | 665 | 16.6 | Lutheran Church (Missouri Synod) |
| Concordia Lutheran Schools of Omaha | Omaha | K-12 | 606 | 15.3 | Lutheran Church (Missouri Synod) |
| Lifegate Christian School | Omaha | K-8 | 499 | 18.1 | Christian (nondenominational) |
| Omaha Christian Academy | Omaha | PreK-12 | 370 | 11.6 | Christian (nondenominational) |
| Lincoln Lutheran Middle/High School | Lincoln | 6-12 | 321 | 13 | Lutheran Church (Missouri Synod) |
| Christ Lutheran School | Norfolk | PreK-8 | 288 | 14.8 | Lutheran Church (Missouri Synod) |
| Nebraska Christain Schools | Central City | PreK-12 | 247 | 13.5 | Christian (nondenominational) |
| College View Academy | Lincoln | K-12 | 233 | 14.2 | Seventh-Day Adventist |
| Parkview Christian Elementary | Lincoln | PreK-12 | 221 | 9.2 | Christian (nondenominational) |
| St. John Lutheran School | Seward | K-8 | 182 | 15.3 | Lutheran Church (Missouri Synod) |
| Messiah Lutheran School | Lincoln | PreK-5 | 179 | 14.9 | Lutheran Church (Missouri Synod) |
| Christ Elementary School | Lincoln | K-5 | 174 | 15 | Lutheran Church (Missouri Synod) |
| First Baptist School | Plattsmouth | K-12 | 143 | 8.9 | Baptist |
| Immanuel Lutheran School | Columbus | PreK-8 | 142 | 14.2 | Lutheran Church (Missouri Synod) |
| Zion Lutheran School | Kearney | PreK-8 | 134 | 16.8 | Lutheran Church (Missouri Synod) |
| Emmanuel-Faith Lutheran School | York | K-8 | 127 | 13.5 | Lutheran Church (Missouri Synod) |
| Lutheran High Northeast | Norfolk | 9-12 | 123 | 9.6 | Lutheran Church (Missouri Synod) |
| St. John Lutheran School | Battle Creek | PreK-8 | 123 | 11.9 | Lutheran Church (Missouri Synod) |
| Trinity Lutheran Elementary School | Fremont | PreK-8 | 122 | 10.8 | Lutheran Church (Missouri Synod) |
| Zion Lutheran School | Pierce | PreK-8 | 112 | 18.7 | Lutheran Church (Missouri Synod) |
| St. Pauls Lutheran School | Beatrice | PreK-5 | 98 | 12.9 | Lutheran Church (Missouri Synod) |
| Faith Christian School | Kearney | PreK-8 | 95 | 8.2 | Christian (nondenominational) |
| Trinity Lutheran Church & School | Lincoln | PreK-5 | 95 | 12.8 | Lutheran Church (Missouri Synod) |
| Immanuel Evangelical Lutheran School | Alliance | PreK-9 | 92 | 10.3 | Lutheran Church (Missouri Synod) |
| Faith Lutheran School | Lincoln | K-5 | 82 | 11.2 | Lutheran Church (Missouri Synod) |
| St. Pauls Lutheran School | Norfolk | PreK-8 | 77 | 9.6 | Wisconsin Evangelical Lutheran Synod |
| St. Mark Elementary School | Lincoln | K-8 | 76 | 15.2 | Evangelical Lutheran Church in America |
| St. Mark Lutheran School | Lincoln | PreK-8 | 76 | 15.2 | Wisconsin Evangelical Lutheran Synod |
| Christ Lutheran School | Juniata | PreK-8 | 72 | 10.1 | Lutheran Church (Missouri Synod) |
| Gethsemane Lutheran School | Omaha | PreK-8 | 66 | 12.2 | Wisconsin Evangelical Lutheran Synod |
| St. Paul Lutheran School | Arlington | PreK-8 | 66 | 9.6 | Lutheran Church (Missouri Synod) |
| St. Paul's Lutheran School | Plymouth | PreK-8 | 66 | 16.1 | Wisconsin Evangelical Lutheran Synod |
| Community Christian School of Western Nebraska | Scottsbluff | PreK-8 | 66 | 7.1 | Christian (nondenominational) |
| Good Shepherd Lutheran School | Omaha | PreK-8 | 62 | 14.1 | Wisconsin Evangelical Lutheran Synod |
| Heartland Lutheran High School | Grand Island | 9-12 | 60 | 9.2 | Lutheran Church (Missouri Synod) |
| Nebraska Evangelical Lutheran High School | Waco | 9-12 | 60 | 7.2 | Wisconsin Evangelical Lutheran Synod |
| Our Redeemer Lutheran School | North Platte | PreK-8 | 59 | 11.8 | Lutheran Church (Missouri Synod) |
| Deshler Lutheran School | Deshler | K-8 | 58 | 11.4 | Lutheran Church (Missouri Synod) |
| St. Paul Lutheran School | Utica | PreK-8 | 56 | 9.3 | Lutheran Church (Missouri Synod) |
| St. Johns Lutheran School | Columbus | K-8 | 56 | 14 | Lutheran Church (Missouri Synod) |