| St. Francis Catholic School | Billings | K-8 | 603 | 13.1 | Roman Catholic |
| Billings Christian School | Billings | PreK-12 | 443 | 7.9 | Christian (nondenominational) |
| St. Labre Schools | Ashland | PreK-12 | 422 | 5.1 | Roman Catholic |
| Stillwater Christian School | Kalispell | PreK-12 | 380 | 10.7 | Christian (nondenominational) |
| Butte Central Elementary School | Butte | PreK-12 | 372 | 13.3 | Roman Catholic |
| Valley Christian School | Missoula | PreK-12 | 326 | 10.9 | Christian (nondenominational) |
| Manhattan Christian School | Manhattan | PreK-12 | 295 | 11.4 | Christian (nondenominational) |
| St. Joseph School | Missoula | PreK-8 | 283 | 12.4 | Roman Catholic |
| Trinity Lutheran School | Billings | PreK-8 | 219 | 20.9 | Lutheran Church (Missouri Synod) |
| Trinity Lutheran School | Kalispell | PreK-8 | 219 | 14.5 | Lutheran Church (Missouri Synod) |
| Foothills Community Christian High School | Great Falls | PreK-12 | 212 | 11.8 | Christian (nondenominational) |
| Helena Christian School | East Helena | PreK-12 | 203 | 13.7 | Christian (nondenominational) |
| St. Andrew School | Helena | PreK-12 | 193 | 6.3 | Roman Catholic |
| St. Matthew's School | Kalispell | PreK-8 | 177 | 8.8 | Roman Catholic |
| Our Lady of Lourdes Catholic School | Great Falls | PreK-8 | 173 | 13.5 | Roman Catholic |
| Sacred Heart School | Miles City | PreK-8 | 160 | 16.2 | Roman Catholic |
| Sacred Heart Elementary School | Miles City | PreK-8 | 159 | 16.6 | Roman Catholic |
| Missoula International School | Missoula | PreK-8 | 150 | 8.9 | Nonsectarian |
| Mission Valley Christian Academy | Polson | PreK-12 | 138 | 7.5 | Christian (nondenominational) |
| Brightways Global Academy | Missoula | PreK-12 | 134 | not reported | Nonsectarian |
| Sussex School | Missoula | K-8 | 125 | 7.6 | Nonsectarian |
| Whitefish Christian Academy | Whitefish | PreK-8 | 116 | 6.7 | Christian (nondenominational) |
| St. Jude Thaddeus School | Havre | PreK-8 | 113 | 11.2 | Roman Catholic |
| St. Marys Catholic School | Livingston | PreK-8 | 101 | 7.2 | Roman Catholic |
| Pretty Eagle Cthlc Schl | Saint Xavier | PreK-8 | 100 | 9.2 | Roman Catholic |
| Kootenai Valley Christian School | Libby | PreK-12 | 95 | 10 | Christian (nondenominational) |
| Grace Montessori Academy | Billings | PreK-8 | 91 | 8.6 | Christian (nondenominational) |
| Hamilton Christian Academy | Hamilton | K-12 | 87 | 12.8 | Assembly of God |
| Pines Academy | Pinesdale | K-8 | 80 | 6.4 | Christian (nondenominational) |
| Acton Academy Hamilton and Curious Minds Montessor | Hamilton | PreK-9 | 74 | 10.6 | Nonsectarian |
| Fairfield Mennonite School | Fairfield | PreK-10 | 74 | 14.8 | Mennonite |
| Middle Creek Montessori | Bozeman | PreK-6 | 72 | 4.6 | Nonsectarian |
| St. Charles Mission School | Pryor | PreK-8 | 70 | 7.8 | Roman Catholic |
| Mt Ellis Elementary | Bozeman | PreK-8 | 65 | 12.3 | Seventh-Day Adventist |
| St. Labre Catholic Elementary School | Ashland | PreK-4 | 61 | 5.5 | Roman Catholic |
| Divine Mercy Academy | Belgrade | PreK-12 | 55 | 5.5 | Roman Catholic |
| Treasure State Academy | Great Falls | PreK-12 | 54 | 10.8 | Baptist |
| Bozeman Summit Schoool | Bozeman | PreK-5 | 52 | 9.6 | Nonsectarian |
| Big Sky Discovery School | Big Sky | PreK-12 | 52 | 3.6 | Nonsectarian |
| Sunrise Montessori School | Billings | PreK-6 | 51 | 4 | Nonsectarian |