| Albuquerque Academy | Albuquerque | 6-12 | 1,185 | 9.5 | Nonsectarian |
| St. Pius X High School | Albuquerque | 8-12 | 617 | 15.5 | Roman Catholic |
| Sandia Preparatory School | Albuquerque | 6-12 | 504 | 9.5 | Nonsectarian |
| Rehoboth Christian School | Rehoboth | PreK-12 | 434 | 14.1 | Calvinist |
| Oak Grove Classical Academy | Albuquerque | PreK-12 | 428 | 12.1 | Other religious |
| Mesilla Valley Christian School | Las Cruces | K-12 | 423 | 13.7 | Christian (nondenominational) |
| Gateway Christian School | Roswell | PreK-12 | 399 | 14 | Christian (nondenominational) |
| Bosque School | Albuquerque | 6-12 | 380 | 8.3 | Nonsectarian |
| Santa Fe Preparatory School | Santa Fe | 7-12 | 343 | 9.4 | Nonsectarian |
| Navajo Preparatory School | Farmington | 9-12 | 282 | 11.1 | Nonsectarian |
| United World College | Montezuma | 11-12 | 222 | 7.1 | Nonsectarian |
| 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) |
| Salem Academy | Albuquerque | PreK-12 | 141 | 14.1 | Islamic |
| Salam Academy | Albuquerque | PreK-12 | 137 | 13.7 | Islamic |
| Grace Baptist Academy | Farmington | PreK-12 | 114 | 15.4 | Baptist |
| Axiom Christian Classical School | Albuquerque | K-12 | 102 | 7.2 | Christian (nondenominational) |
| Paradise Christian School | Albuquerque | K-12 | 99 | 9.6 | Christian (nondenominational) |
| Mission Academy | Las Cruces | K-12 | 79 | 10.4 | Nonsectarian |
| Generations Academy | Portales | PreK-12 | 77 | 8.5 | Christian (nondenominational) |
| Calvary Christian Academy | Silver City | PreK-12 | 70 | 5.9 | Christian (nondenominational) |
| Evangel Christian Academy | Albuquerque | K-12 | 67 | 9.9 | Assembly of God |
| Acton Albuquerque | Albuquerque | K-12 | 64 | 16 | Nonsectarian |
| Faith Christian Academy | Carlsbad | 1-12 | 63 | 12.6 | Baptist |
| DLD Sycamore School | Albuquerque | 2-12 | 60 | 4.9 | Nonsectarian |
| 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 |
| Farmington Mennonite School | Farmington | 1-9 | 43 | 8.6 | Mennonite |
| Faith Christian Academy | Farmington | K-12 | 42 | 9.8 | Baptist |
| Abundant Life Christian School | Albuquerque | PreK-10 | 32 | 5 | Mennonite |
| Wildcat Christian Academy | Gallup | K-12 | 32 | 5.3 | 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) |
| Valley Baptist Academy | Espanola | 1-12 | 20 | 5 | Christian (nondenominational) |
| Pathways Academy | Albuquerque | 2-12 | 20 | 5 | Nonsectarian |
| La Vida Mission School | Farmington | K-12 | 19 | 3 | Seventh-Day Adventist |