| Ss Peter & Paul Ukrainian Catholic School | 13.4 |
Regular elementary or secondary | KG-8 | 102 | 10.4 | Roman Catholic |
| St Joseph School | 14.2 |
Regular elementary or secondary | 1-8 | 163 | 11.8 | Roman Catholic |
| Clyde Mennonite Parochial School | 14.4 |
Regular elementary or secondary | 1-8 | 36 | 12.4 | Mennonite |
| Montessori School Of The Finger Lakes | 14.7 |
Montessori | Pre-KG-5 | 18 | 2.5 | Christian (no specific denomination) |
| Word Of Life Christian Academy | 17.1 |
Regular elementary or secondary | Pre-KG-5 | 35 | 8.8 | Assembly of God |
| St Mary's Academy | 17.1 |
Regular elementary or secondary | Pre-KG-6 | 134 | 14.3 | Roman Catholic |
| Frontenac Sda Elementary School | 19.1 |
Regular elementary or secondary | 2-8 | 11 | 10.0 | Seventh-Day Adventist |
| The Bishops Academy At Holy Family | 22.2 |
Regular elementary or secondary | Pre-KG-6 | 241 | 13.8 | Roman Catholic |
| St Michael Elementary School | 22.3 |
Regular elementary or secondary | Pre-KG-8 | 118 | 10.2 | Roman Catholic |
| Fayette Mennonite School | 23.1 |
Regular elementary or secondary | 1-8 | 37 | 12.3 | Mennonite |
| Children's Hours School | 23.6 |
Alternative/other | Pre-KG-1 | 7 | 2.1 | Nonsectarian |
| St Francis De Sales-st Stephen | 23.9 |
Regular elementary or secondary | Pre-KG-8 | 158 | 13.6 | Roman Catholic |
| Bishop's Academy At St Charles Borromeo | 24.1 |
Regular elementary or secondary | Pre-KG-6 | 130 | 10.3 | Roman Catholic |
| Trinity Catholic School | 24.6 |
Regular elementary or secondary | Pre-KG-6 | 107 | 8.9 | Roman Catholic |
| East Palmyra Christian School | 24.9 |
Regular elementary or secondary | Pre-KG-8 | 60 | 8.8 | Christian (no specific denomination) |
