| Cole Valley Christian Schools-Secondary | Meridian | PreK-12 | 1,263 | 15.8 | Christian (nondenominational) |
| Logos Online School | Moscow | 7-12 | 1,200 | 23.1 | Christian (nondenominational) |
| Nampa Christian High School | Nampa | PreK-12 | 889 | 15.5 | Christian (nondenominational) |
| Nampa Christian Schools, Inc | Nampa | PreK-12 | 889 | 15.5 | Christian (nondenominational) |
| Genesis Preparatory Academy | Post Falls | PreK-12 | 541 | 15.8 | Christian (nondenominational) |
| Genesis Prep Academy | Post Falls | PreK-12 | 466 | 11 | Christian (nondenominational) |
| Grace Lutheran School | Pocatello | PreK-12 | 430 | 9.2 | Lutheran Church (Missouri Synod) |
| Watersprings School | Idaho Falls | PreK-12 | 364 | 12.3 | Christian (nondenominational) |
| Lighthouse Christian School | Twin Falls | PreK-12 | 305 | 14.9 | Christian (nondenominational) |
| Christian Center School | Hayden | PreK-12 | 230 | 13.1 | Christian (nondenominational) |
| Greenleaf Friends Academy | Greenleaf | K-12 | 228 | 14 | Friends |
| North Idaho Christian School | Hayden | K-12 | 228 | 14 | Christian (nondenominational) |
| Calvary Christian School | Boise | PreK-8 | 223 | 13.2 | Christian (nondenominational) |
| Classical Christian Academy | Rathdrum | PreK-12 | 212 | 10 | Christian (nondenominational) |
| Immanuel Lutheran School | Twin Falls | PreK-5 | 186 | 16.5 | Lutheran Church (Missouri Synod) |
| Calvary Meridian Prep Academy | Meridian | K-10 | 185 | 15 | Christian (nondenominational) |
| Lake City Academy | Coeur D Alene | PreK-8 | 140 | 14.7 | Seventh-Day Adventist |
| House of the Lord Christian Academy | Oldtown | PreK-12 | 130 | 8.4 | Christian (nondenominational) |
| Calvary Christian Academy | Emmett | PreK-12 | 123 | 8.4 | Christian (nondenominational) |
| Sandpoint Christian School | Ponderay | PreK-8 | 121 | 17.3 | Christian (nondenominational) |
| Summit Christian Academy | Coeur D Alene | PreK-6 | 107 | 11.3 | Christian (nondenominational) |
| Cornerstone Christian School | Lewiston | K-8 | 107 | 10.1 | Christian (nondenominational) |
| Pine Grove Academy | Post Falls | PreK-8 | 102 | 7.4 | Latter Day Saints |
| Gem State Adventist Academy | Caldwell | 9-12 | 83 | 10.9 | Seventh-Day Adventist |
| Mountain View Christian School | Bonners Ferry | 1-8 | 79 | 10.5 | Mennonite |
| Boise Valley Adventist School | Boise | PreK-8 | 75 | 12.9 | Seventh-Day Adventist |
| Calvary Christian School | Nampa | PreK-12 | 73 | 13.8 | Christian (nondenominational) |
| Canyonside Christian School | Jerome | PreK-6 | 65 | 6 | Christian (nondenominational) |
| Joshua Institute Academy | Meridian | 3-12 | 56 | 8 | Christian (nondenominational) |
| Caldwell Adventist Elementary | Caldwell | PreK-8 | 52 | 13 | Seventh-Day Adventist |
| Hope Lutheran School | Idaho Falls | PreK-7 | 45 | 6.9 | Lutheran Church (Missouri Synod) |
| Canyon Christian School | Hazelton | 1-8 | 42 | 7.8 | Mennonite |
| Lewis Clark Christian | Lewiston | K-12 | 39 | 6.7 | Christian (nondenominational) |
| River of Life Christian School | Payette | PreK-12 | 38 | 7.6 | Christian (nondenominational) |
| Wild Rose Christian School | Viola | K-8 | 38 | 6.3 | Mennonite |
| Sandpoint Jr Academy | Sandpoint | 1-8 | 36 | 10.6 | Seventh-Day Adventist |
| Silver Valley Christian Academy | Kellogg | PreK-12 | 35 | 35 | Christian (nondenominational) |
| Deep Creek Mennonite School | Buhl | 1-8 | 29 | 4.1 | Mennonite |
| Clear Lakes Christian Academy | Buhl | K-11 | 25 | 8.9 | Christian (nondenominational) |
| Waymaker Christian Academy | Coeur D Alene | Transitional 1st-11 | 25 | 4.5 | Christian (nondenominational) |