| Rehoboth Christian School | Rehoboth | PreK-12 | 434 | 14.1 | Calvinist |
| Mesilla Valley Christian School | Las Cruces | K-12 | 423 | 13.7 | Christian (nondenominational) |
| Gateway Christian School | Roswell | PreK-12 | 399 | 14 | Christian (nondenominational) |
| Gospel Light Baptist Academy | Rio Rancho | K-12 | 221 | 11.1 | Baptist |
| Canon Christian Academy | Belen | PreK-12 | 218 | 11.6 | Christian (nondenominational) |
| Clovis Christian Schools | Clovis | PreK-12 | 208 | 5.1 | Christian (nondenominational) |
| Calvary Christian Academy | Albuquerque | PreK-12 | 150 | 6.6 | Christian (nondenominational) |
| Grace Baptist Academy | Farmington | PreK-12 | 114 | 15.4 | Baptist |
| Christ Lutheran School | Albuquerque | PreK-8 | 111 | 8.8 | Lutheran Church (Missouri Synod) |
| Axiom Christian Classical School | Albuquerque | K-12 | 102 | 7.2 | Christian (nondenominational) |
| Paradise Christian School | Albuquerque | K-12 | 99 | 9.6 | Christian (nondenominational) |
| East Gate Kids Early Learning Center | Albuquerque | PreK-7 | 93 | 21.1 | Church of Christ |
| Junction Christian Academy | Hobbs | PreK-5 | 92 | 13.1 | Christian (nondenominational) |
| Generations Academy | Portales | PreK-12 | 77 | 8.5 | Christian (nondenominational) |
| Western Heights Learning Center | Albuquerque | PreK-5 | 73 | 12.2 | Assembly of God |
| Zuni Christian Mission School | Zuni | K-8 | 72 | 9.5 | Calvinist |
| Eastern Hills Christian Academy | Albuquerque | PreK-8 | 71 | 7.6 | Christian (nondenominational) |
| Calvary Christian Academy | Silver City | PreK-12 | 70 | 5.9 | Christian (nondenominational) |
| Albuquerque Christian School | Albuquerque | PreK-6 | 70 | 9.5 | Christian (nondenominational) |
| Evangel Christian Academy | Albuquerque | K-12 | 67 | 9.9 | Assembly of God |
| Acts Christian Academy | Farmington | PreK-8 | 66 | 9.4 | Church of the Nazarene |
| Immanuel Lutheran School | Albuquerque | PreK-8 | 66 | 7.3 | Lutheran Church (Missouri Synod) |
| Faith Christian Academy | Carlsbad | 1-12 | 63 | 12.6 | Baptist |
| Cross of Hope School | Albuquerque | PreK-5 | 56 | 6 | Lutheran Church (Missouri Synod) |
| Immanuel Lutheran School | Roswell | PreK-9 | 54 | 9 | Lutheran Church (Missouri Synod) |
| Tower Road Christian Academy | Albuquerque | PreK-11 | 50 | 6.3 | Baptist |
| Sandia View Academy | Corrales | 9-12 | 47 | 8.9 | Seventh-Day Adventist |
| Shepherd Lutheran | Albuquerque | K-8 | 46 | 15.3 | Wisconsin Evangelical Lutheran Synod |
| Farmington Mennonite School | Farmington | 1-9 | 43 | 8.6 | Mennonite |
| Faith Christian Academy | Farmington | K-12 | 42 | 9.8 | Baptist |
| Mission Lutheran School | Las Cruces | PreK-6 | 37 | 9 | Lutheran Church (Missouri Synod) |
| Artesia Classical Academy | Artesia | K-6 | 33 | 7.3 | Christian (nondenominational) |
| Abundant Life Christian School | Albuquerque | PreK-10 | 32 | 5 | Mennonite |
| Wildcat Christian Academy | Gallup | K-12 | 32 | 5.3 | Christian (nondenominational) |
| College Heights Kindergarten | Las Cruces | PreK-Transitional K | 30 | 9.1 | Christian (nondenominational) |
| Veritas Classical Christian Academy | Hobbs | PreK-12 | 30 | 6 | Christian (nondenominational) |
| Open Bible Christian Academy | Waterflow | K-12 | 28 | 5.8 | Baptist |
| Legacy Christian Academy | Alamogordo | PreK-12 | 27 | 3.6 | Christian (nondenominational) |
| Canyon Christian Academy | Alamogordo | PreK-4 | 22 | 11 | Seventh-Day Adventist |
| Valley Baptist Academy | Espanola | 1-12 | 20 | 5 | Christian (nondenominational) |