| St. Wenceslaus School | Omaha | PreK-8 | 793 | 28.4 | Roman Catholic |
| St. Vincent de Paul School | Omaha | K-8 | 732 | 19.2 | Roman Catholic |
| Concordia Jr.-Sr. High School | Omaha | K-12 | 665 | 16.6 | Lutheran Church (Missouri Synod) |
| St. Stephen the Martyr Catholic School | Omaha | PreK-8 | 648 | 19 | Roman Catholic |
| St. Pius X/St. Leo Elementary School | Omaha | PreK-8 | 633 | 14.7 | Roman Catholic |
| Concordia Lutheran Schools of Omaha | Omaha | K-12 | 606 | 15.3 | Lutheran Church (Missouri Synod) |
| Mary Our Queen School | Omaha | PreK-8 | 532 | 13.1 | Roman Catholic |
| St. Robert Bellarmine School | Omaha | PreK-8 | 516 | 16.1 | Roman Catholic |
| St. Columbkille Catholic School | Papillion | PreK-8 | 511 | 20.6 | Roman Catholic |
| Lifegate Christian School | Omaha | K-8 | 499 | 18.1 | Christian (nondenominational) |
| St. Margaret Mary School | Omaha | K-8 | 497 | 18 | Roman Catholic |
| Brownell Talbot College Preparatory School | Omaha | PreK-12 | 436 | 8.9 | Nonsectarian |
| Archbishop Bergan Catholic School | Fremont | PreK-12 | 428 | 12.2 | Roman Catholic |
| St. James Seton School | Omaha | PreK-8 | 417 | 16.3 | Roman Catholic |
| St. Joseph School | Lincoln | PreK-8 | 414 | 13.4 | Roman Catholic |
| North American Martyrs School | Lincoln | PreK-8 | 402 | 17.3 | Roman Catholic |
| Scotus Central Catholic High School | Columbus | 7-12 | 375 | 13.3 | Roman Catholic |
| Omaha Christian Academy | Omaha | PreK-12 | 370 | 11.6 | Christian (nondenominational) |
| Guardian Angels Central Catholic High School | West Point | PreK-12 | 364 | 12.5 | Roman Catholic |
| Kearney Catholic High School | Kearney | 6-12 | 355 | 14.7 | Roman Catholic |
| Catholic High School of Kearney | Kearney | 6-12 | 355 | 14.8 | Roman Catholic |
| St. Patrick Jr Sr High School | North Platte | K-12 | 349 | 9.5 | Roman Catholic |
| St. Patrick High School | North Platte | PreK-12 | 348 | 11.4 | Roman Catholic |
| Duchesne Academy of the Sacred Heart | Omaha | PreK-12 | 326 | 8.8 | Roman Catholic, all-girls |
| Lincoln Lutheran Middle/High School | Lincoln | 6-12 | 321 | 13 | Lutheran Church (Missouri Synod) |
| St. Michael Catholic School | Lincoln | PreK-8 | 312 | 15.5 | Roman Catholic |
| Central Catholic Middle & High School | Grand Island | 6-12 | 302 | 12.5 | Roman Catholic |
| St. John the Apostle Catholic School | Lincoln | PreK-8 | 299 | 13.4 | Roman Catholic |
| St. Gerald School | Ralston | PreK-8 | 292 | 11.7 | Roman Catholic |
| Christ Lutheran School | Norfolk | PreK-8 | 288 | 14.8 | Lutheran Church (Missouri Synod) |
| Lourdes Central Catholic School | Nebraska City | PreK-12 | 282 | 10.5 | Roman Catholic |
| St. Wenceslaus School | Wahoo | PreK-6 | 261 | 14.6 | Roman Catholic |
| Bishop Neumann High School | Wahoo | 7-12 | 261 | 11.1 | Roman Catholic |
| St. Peter Catholic School | Lincoln | PreK-8 | 260 | 13 | Roman Catholic |
| Christ the King School | Omaha | PreK-8 | 256 | 10.2 | Roman Catholic |
| Nebraska Christain Schools | Central City | PreK-12 | 247 | 13.5 | Christian (nondenominational) |
| Ss Peter & Paul Elementary School | Omaha | PreK-8 | 247 | 10 | Roman Catholic |
| Holy Cross School | Omaha | PreK-8 | 244 | 15.2 | Roman Catholic |
| St. Teresa Elementary School | Lincoln | PreK-8 | 238 | 11.6 | Roman Catholic |
| College View Academy | Lincoln | K-12 | 233 | 14.2 | Seventh-Day Adventist |