| Rehoboth Christian School | Rehoboth | PreK-12 | 434 | 14.1 | Calvinist |
| Oak Grove Classical Academy | Albuquerque | PreK-12 | 428 | 12.1 | Other religious |
| Manzano Day School | Albuquerque | PreK-5 | 426 | 11.9 | Nonsectarian |
| Mesilla Valley Christian School | Las Cruces | K-12 | 423 | 13.7 | Christian (nondenominational) |
| Gateway Christian School | Roswell | PreK-12 | 399 | 14 | Christian (nondenominational) |
| Annunciation Catholic School | Albuquerque | PreK-8 | 389 | 11.8 | Roman Catholic |
| St. Thomas Aquinas School | Rio Rancho | PreK-8 | 295 | 12.8 | Roman Catholic |
| Las Cruces Catholic School | Las Cruces | PreK-8 | 274 | 11.7 | Roman Catholic |
| Sunset Mesa School | Albuquerque | PreK-5 | 271 | 11.5 | Nonsectarian |
| St. Mary's School | Albuquerque | PreK-8 | 232 | 9.2 | Roman Catholic |
| 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) |
| St. Mary's Catholic School Belen | Belen | PreK-8 | 151 | 14.4 | Roman Catholic |
| Calvary Christian Academy | Albuquerque | PreK-12 | 150 | 6.6 | Christian (nondenominational) |
| Salem Academy | Albuquerque | PreK-12 | 141 | 14.1 | Islamic |
| Dzilth-Na-O-Dith-Hle Community Grant School | Bloomfield | K-8 | 140 | 10 | Nonsectarian |
| San Felipe de Neri School | Albuquerque | PreK-8 | 140 | 9.7 | Roman Catholic |
| Rio Grande School | Santa Fe | PreK-6 | 140 | 5.4 | Nonsectarian |
| Santo Ninos Regional Catholic School | Santa Fe | PreK-6 | 137 | 11.4 | Roman Catholic |
| Salam Academy | Albuquerque | PreK-12 | 137 | 13.7 | Islamic |
| Holy Ghost Catholic School | Albuquerque | PreK-8 | 122 | 5 | Roman Catholic |
| Santa Fe School for the Arts & Sciences | Santa Fe | PreK-8 | 120 | 7.9 | Nonsectarian |
| Our Lady of the Assumption Catholic School | Albuquerque | PreK-8 | 118 | 7.9 | Roman Catholic |
| Grace Baptist Academy | Farmington | PreK-12 | 114 | 15.4 | Baptist |
| Christ Lutheran School | Albuquerque | PreK-8 | 111 | 8.8 | Lutheran Church (Missouri Synod) |
| St. Anthony Indian School | Zuni | K-8 | 107 | 8.9 | Roman Catholic |
| Sacred Heart Catholic School | Farmington | PreK-8 | 104 | 7.7 | Roman Catholic |
| Axiom Christian Classical School | Albuquerque | K-12 | 102 | 7.2 | Christian (nondenominational) |
| Paradise Christian School | Albuquerque | K-12 | 99 | 9.6 | Christian (nondenominational) |
| St. Bonaventure School | Thoreau | PreK-8 | 97 | 5.4 | Roman Catholic |
| 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) |
| St. Charles Borromeo Elementary School | Albuquerque | PreK-8 | 88 | 8 | Roman Catholic |
| Escuela del Sol Montessori School | Albuquerque | PreK-8 | 86 | 2.9 | Nonsectarian |
| Holy Child Catholic School | Tijeras | PreK-8 | 81 | 5.4 | Nonsectarian |
| St. Helena School of Hobbs | Hobbs | PreK-5 | 79 | 13.2 | Roman Catholic |
| Mission Academy | Las Cruces | K-12 | 79 | 10.4 | Nonsectarian |
| Generations Academy | Portales | PreK-12 | 77 | 8.5 | Christian (nondenominational) |
| St. Teresa of Avila Catholic School | Grants | PreK-8 | 75 | 12.7 | Roman Catholic |