| St James The Greater School | 0.0 |
Regular elementary or secondary | Pre-KG-5 | 91 | 9.2 | Roman Catholic |
| Eau Claire Lutheran School | 1.0 |
Regular elementary or secondary | KG-8 | 77 | 11.8 | Lutheran Church - Missouri Synod |
| Immaculate Conception Elementary School | 2.6 |
Regular elementary or secondary | KG-5 | 222 | 13.5 | Roman Catholic |
| Messiah Lutheran School | 2.6 |
Regular elementary or secondary | KG-8 | 104 | 15.8 | Other Lutheran |
| Regis Middle School | 2.9 |
Regular elementary or secondary | 6-8 | 172 | 14.8 | Roman Catholic |
| St Mark Lutheran School | 3.0 |
Regular elementary or secondary | KG-8 | 123 | 16.2 | Wisconsin Evangelical Lutheran Synod |
| Crestview Academy | 4.3 |
Regular elementary or secondary | KG-8 | 196 | 12.4 | Christian (no specific denomination) |
| St Mary's Elementary School | 4.4 |
Regular elementary or secondary | Pre-KG-5 | 85 | 12.3 | Roman Catholic |
| St Charles/holy Ghost Schools | 9.4 |
Regular elementary or secondary | Pre-KG-6 | 213 | 10.7 | Roman Catholic |
| Peru Amish School | 11.3 |
Regular elementary or secondary | 1-8 | 21 | 21.0 | Amish |
| St Peter Elementary School | 13.3 |
Regular elementary or secondary | 1-8 | 54 | 11.2 | Roman Catholic |
| Albany Hill's School | 15.1 |
Regular elementary or secondary | 1-8 | 25 | 25.0 | Amish |
| Duscham Amish School | 16.8 |
Regular elementary or secondary | 1-8 | 16 | 16.0 | Amish |
| Valley View Amish School | 17.8 |
Regular elementary or secondary | 1-8 | 24 | 24.0 | Amish |
| Menomonie Alliance Christian School | 19.1 |
Regular elementary or secondary | KG-8 | 60 | 7.5 | Christian (no specific denomination) |
| St Paul Lutheran School | 19.4 |
Regular elementary or secondary | Pre-KG-8 | 23 | 8.8 | Wisconsin Evangelical Lutheran Synod |
| St Paul Elementary School | 19.5 |
Regular elementary or secondary | Pre-KG-8 | 161 | 13.9 | Roman Catholic |
| St Pauls Lutheran School | 19.7 |
Regular elementary or secondary | Pre-KG-8 | 68 | 10.8 | Wisconsin Evangelical Lutheran Synod |
| St Joseph Grade School | 19.7 |
Regular elementary or secondary | Pre-KG-6 | 135 | 11.8 | Roman Catholic |
| Augusta Mennonite School | 19.9 |
Regular elementary or secondary | 1-8 | 22 | 8.5 | Mennonite |
| St Joseph School | 20.2 |
Regular elementary or secondary | Pre-KG-8 | 37 | 5.9 | Roman Catholic |
| Plain View School | 22.3 |
Regular elementary or secondary | 1-6 | 21 | 21.0 | Amish |
| Oakridge School | 24.0 |
Regular elementary or secondary | 1-6 | 23 | 23.0 | Amish |
| Amish School 5 | 24.9 |
Regular elementary or secondary | 1-6 | 22 | 11.0 | Amish |
