| Grace Lutheran School | 0.0 |
Regular elementary or secondary | Pre-KG-4 | 16 | 5.3 | Lutheran Church - Missouri Synod |
| Maranatha Adventist School | 0.8 |
Regular elementary or secondary | 4-8 | 13 | 6.5 | Seventh-Day Adventist |
| Rochester Montessori School | 15.5 |
Montessori | Pre-KG-6 | 62 | 5.7 | Nonsectarian |
| St Isidore Elementary School | 17.5 |
Regular elementary or secondary | Pre-KG-5 | 15 | 7.1 | Roman Catholic |
| Resurrection Lutheran School | 18.2 |
Regular elementary or secondary | KG-8 | 119 | 18.9 | Wisconsin Evangelical Lutheran Synod |
| Owatonna Montessori Childrens House | 18.4 |
Montessori | Pre-KG-KG | 7 | 7.0 | Nonsectarian |
| St Pius X School | 18.6 |
Regular elementary or secondary | KG-4 | 231 | 17.0 | Roman Catholic |
| St Mary's - Marian | 18.7 |
Regular elementary or secondary | Pre-KG-8 | 366 | 14.9 | Roman Catholic |
| St Marys School | 18.7 |
Regular elementary or secondary | Pre-KG-8 | 366 | 15.5 | Roman Catholic |
| Rochester Central Lutheran School | 18.9 |
Regular elementary or secondary | Pre-KG-8 | 276 | 12.7 | Lutheran Church - Missouri Synod |
| St Francis Of Assisi Elementary School | 20.2 |
Regular elementary or secondary | Pre-KG-8 | 407 | 18.2 | Roman Catholic |
| Christ Lutheran School | 20.4 |
Regular elementary or secondary | KG-8 | 50 | 12.8 | Wisconsin Evangelical Lutheran Synod |
| Greene Valley School | 21.7 |
Regular elementary or secondary | KG-8 | 23 | 12.1 | Seventh-Day Adventist |
| Holy Spirit School | 24.4 |
Regular elementary or secondary | KG-8 | 328 | 15.7 | Roman Catholic |
