| St Charles/holy Ghost Schools | 5.1 |
Regular elementary or secondary | Pre-KG-6 | 213 | 10.7 | Roman Catholic |
| St Paul Lutheran School | 7.1 |
Regular elementary or secondary | Pre-KG-8 | 23 | 8.8 | Wisconsin Evangelical Lutheran Synod |
| St Paul Elementary School | 7.3 |
Regular elementary or secondary | Pre-KG-8 | 161 | 13.9 | Roman Catholic |
| Messiah Lutheran School | 11.8 |
Regular elementary or secondary | KG-8 | 104 | 15.8 | Other Lutheran |
| Crestview Academy | 12.0 |
Regular elementary or secondary | KG-8 | 196 | 12.4 | Christian (no specific denomination) |
| Eau Claire Lutheran School | 13.0 |
Regular elementary or secondary | KG-8 | 77 | 11.8 | Lutheran Church - Missouri Synod |
| Sunny Meadow Amish School | 13.2 |
Regular elementary or secondary | 1-8 | 24 | 15.0 | Amish |
| St James The Greater School | 13.3 |
Regular elementary or secondary | Pre-KG-5 | 91 | 9.2 | Roman Catholic |
| St Mary's Elementary School | 13.8 |
Regular elementary or secondary | Pre-KG-5 | 85 | 12.3 | Roman Catholic |
| Immaculate Conception Elementary School | 13.8 |
Regular elementary or secondary | KG-5 | 222 | 13.5 | Roman Catholic |
| Regis Middle School | 14.1 |
Regular elementary or secondary | 6-8 | 172 | 14.8 | Roman Catholic |
| St Joseph School | 14.5 |
Regular elementary or secondary | Pre-KG-8 | 37 | 5.9 | Roman Catholic |
| St Mark Lutheran School | 15.5 |
Regular elementary or secondary | KG-8 | 123 | 16.2 | Wisconsin Evangelical Lutheran Synod |
| Twin Lakes Amish School | 16.8 |
Regular elementary or secondary | 1-7 | 23 | 14.4 | Amish |
| Pleasant View Amish School | 18.2 |
Regular elementary or secondary | 1-8 | 35 | 31.8 | Amish |
| Augusta Mennonite School | 23.5 |
Regular elementary or secondary | 1-8 | 22 | 8.5 | Mennonite |
| Amish School | 24.0 |
Regular elementary or secondary | 1-4 | 10 | 10.0 | Amish |
| Menomonie Alliance Christian School | 24.3 |
Regular elementary or secondary | KG-8 | 60 | 7.5 | Christian (no specific denomination) |
| Peru Amish School | 24.4 |
Regular elementary or secondary | 1-8 | 21 | 21.0 | Amish |
