| Duscham Amish School | 2.3 |
Regular elementary or secondary | 1-8 | 16 | 16.0 | Amish |
| Peru Amish School | 4.2 |
Regular elementary or secondary | 1-8 | 21 | 21.0 | Amish |
| Valley View Amish School | 4.3 |
Regular elementary or secondary | 1-8 | 24 | 24.0 | Amish |
| Assumption Catholic School | 12.4 |
Regular elementary or secondary | Pre-KG-8 | 136 | 10.2 | Roman Catholic |
| Thompson Lake Christian School | 13.3 |
Regular elementary or secondary | 3-8 | 8 | 8.0 | Seventh-Day Adventist |
| St Mark Lutheran School | 14.2 |
Regular elementary or secondary | KG-8 | 123 | 16.2 | Wisconsin Evangelical Lutheran Synod |
| Eau Claire Lutheran School | 15.0 |
Regular elementary or secondary | KG-8 | 77 | 11.8 | Lutheran Church - Missouri Synod |
| St James The Greater School | 15.1 |
Regular elementary or secondary | Pre-KG-5 | 91 | 9.2 | Roman Catholic |
| Immaculate Conception Elementary School | 15.9 |
Regular elementary or secondary | KG-5 | 222 | 13.5 | Roman Catholic |
| Regis Middle School | 15.9 |
Regular elementary or secondary | 6-8 | 172 | 14.8 | Roman Catholic |
| St Mary's Elementary School | 17.4 |
Regular elementary or secondary | Pre-KG-5 | 85 | 12.3 | Roman Catholic |
| Messiah Lutheran School | 17.4 |
Regular elementary or secondary | KG-8 | 104 | 15.8 | Other Lutheran |
| St Pauls Lutheran School | 17.5 |
Regular elementary or secondary | Pre-KG-8 | 68 | 10.8 | Wisconsin Evangelical Lutheran Synod |
| St Joseph Grade School | 17.6 |
Regular elementary or secondary | Pre-KG-6 | 135 | 11.8 | Roman Catholic |
| Menomonie Alliance Christian School | 17.9 |
Regular elementary or secondary | KG-8 | 60 | 7.5 | Christian (no specific denomination) |
| Crestview Academy | 18.5 |
Regular elementary or secondary | KG-8 | 196 | 12.4 | Christian (no specific denomination) |
| St Charles/holy Ghost Schools | 24.4 |
Regular elementary or secondary | Pre-KG-6 | 213 | 10.7 | Roman Catholic |
| St Boniface School | 24.7 |
Regular elementary or secondary | Pre-KG-8 | 36 | 8.4 | Roman Catholic |
