| Emmanuel Baptist Christian Academy | 3.1 |
Regular elementary or secondary | KG-12 | 127 | 7.9 | Baptist |
| Bible Baptist School | 3.6 |
Regular elementary or secondary | Pre-KG-12 | 441 | 13.0 | Baptist |
| Harrisburg Academy | 4.0 |
Regular elementary or secondary | Pre-KG-12 | 403 | 9.8 | Nonsectarian |
| Wordsworth Academy | 5.6 |
Special education | 2-12 | 47 | 7.8 | Nonsectarian |
| Hillside Amish School | 6.9 |
Regular elementary or secondary | 1-9 | 19 | 19.0 | Amish |
| Covenant Christian Academy | 11.2 |
Regular elementary or secondary | KG-12 | 198 | 11.1 | Christian (no specific denomination) |
| Harrisburg Christian School | 11.3 |
Regular elementary or secondary | KG-12 | 282 | 11.6 | Christian (no specific denomination) |
| Yellow Breeches Education Center | 11.4 |
Special education | 6-12 | 88 | 6.3 | Nonsectarian |
| Bethel Christian Academy | 12.8 |
Regular elementary or secondary | KG-12 | 135 | 7.9 | Christian (no specific denomination) |
| Armstrong Valley Christian School | 16.9 |
Regular elementary or secondary | Ungraded-Ungraded | 22 | 7.3 | Baptist |
| Hershey Christian School | 17.0 |
Regular elementary or secondary | KG-12 | 280 | 11.1 | Christian (no specific denomination) |
| Greater Perry Community Christian Academy | 17.2 |
Regular elementary or secondary | KG-10 | 23 | 5.6 | Christian (no specific denomination) |
| Kralltown Mennonite School | 19.0 |
Alternative/other | 1-9 | 30 | 30.0 | Mennonite |
| Milton Hershey School | 19.0 |
Regular elementary or secondary | Pre-KG-12 | 1695 | 8.8 | Nonsectarian |
| Bible Baptist Christian School | 19.0 |
Regular elementary or secondary | Pre-KG-12 | 121 | 8.6 | Baptist |
| Mt Calvary Christian School | 21.4 |
Regular elementary or secondary | Pre-KG-12 | 367 | 10.6 | Christian (no specific denomination) |
| Christian School Of York | 22.2 |
Regular elementary or secondary | Pre-KG-12 | 337 | 9.3 | Christian (no specific denomination) |
| York Sda Church School | 22.3 |
Regular elementary or secondary | Pre-KG-9 | 38 | 9.7 | Seventh-Day Adventist |
| Good Will Mennonite School | 24.6 |
Regular elementary or secondary | 1-9 | 30 | 8.3 | Mennonite |
| Faith And Truth Assembly | 24.8 |
Regular elementary or secondary | Pre-KG-10 | 9 | 4.5 | Christian (no specific denomination) |
