| Emmanuel Baptist Christian Academy | 0.5 |
Regular elementary or secondary | KG-12 | 127 | 7.9 | Baptist |
| Harrisburg Academy | 3.2 |
Regular elementary or secondary | Pre-KG-12 | 403 | 9.8 | Nonsectarian |
| Faith Tabernacle School | 3.6 |
Regular elementary or secondary | 1-12 | 152 | 10.4 | Christian (no specific denomination) |
| Wordsworth Academy | 5.8 |
Special education | 2-12 | 47 | 7.8 | Nonsectarian |
| Hillside Amish School | 6.3 |
Regular elementary or secondary | 1-9 | 19 | 19.0 | Amish |
| Covenant Christian Academy | 10.9 |
Regular elementary or secondary | KG-12 | 198 | 11.1 | Christian (no specific denomination) |
| Yellow Breeches Education Center | 11.3 |
Special education | 6-12 | 88 | 6.3 | Nonsectarian |
| Harrisburg Christian School | 12.4 |
Regular elementary or secondary | KG-12 | 282 | 11.6 | Christian (no specific denomination) |
| Bethel Christian Academy | 12.8 |
Regular elementary or secondary | KG-12 | 135 | 7.9 | Christian (no specific denomination) |
| Bible Baptist Christian School | 15.6 |
Regular elementary or secondary | Pre-KG-12 | 121 | 8.6 | Baptist |
| Hershey Christian School | 15.7 |
Regular elementary or secondary | KG-12 | 280 | 11.1 | Christian (no specific denomination) |
| Kralltown Mennonite School | 15.7 |
Alternative/other | 1-9 | 30 | 30.0 | Mennonite |
| Milton Hershey School | 18.0 |
Regular elementary or secondary | Pre-KG-12 | 1695 | 8.8 | Nonsectarian |
| Christian School Of York | 18.7 |
Regular elementary or secondary | Pre-KG-12 | 337 | 9.3 | Christian (no specific denomination) |
| York Sda Church School | 18.7 |
Regular elementary or secondary | Pre-KG-9 | 38 | 9.7 | Seventh-Day Adventist |
| Mt Calvary Christian School | 19.1 |
Regular elementary or secondary | Pre-KG-12 | 367 | 10.6 | Christian (no specific denomination) |
| Armstrong Valley Christian School | 19.5 |
Regular elementary or secondary | Ungraded-Ungraded | 22 | 7.3 | Baptist |
| Greater Perry Community Christian Academy | 20.8 |
Regular elementary or secondary | KG-10 | 23 | 5.6 | Christian (no specific denomination) |
| Faith And Truth Assembly | 21.3 |
Regular elementary or secondary | Pre-KG-10 | 9 | 4.5 | Christian (no specific denomination) |
| Bethel Christian Academy | 21.6 |
Regular elementary or secondary | KG-12 | 21 | 6.8 | Christian (no specific denomination) |
| Tidings Of Peace Christian School | 22.0 |
Regular elementary or secondary | KG-12 | 34 | 5.6 | Mennonite |
| Paradise School For Boys | 22.5 |
Alternative/other | 1-12 | 70 | 8.4 | Roman Catholic |
| York Country Day School | 22.6 |
Regular elementary or secondary | Pre-KG-12 | 168 | 6.0 | Nonsectarian |
| Montessori Childrens House | 23.1 |
Montessori | Ungraded-Ungraded | 85 | 12.1 | Nonsectarian |
| Pleasant Hill Christian School | 23.5 |
Regular elementary or secondary | 1-12 | 47 | 11.8 | Brethren |
