| 29 | Hillfield Strathallan College | Hamilton | Online/Site Based | Conference of Independent Schools of Ontario | Visit |
| 120 | Lyonsgate Montessori School | Hamilton | Site based only | Canadian Council of Montessori Administrators (CCMA) | Visit |
| 174 | Calvin Christian School | Hamilton | Site based only | EDVance | Visit |
| 297 | Timothy Canadian Reformed School | Hamilton | Site based only | The League of Canadian Reformed School Societies | — |
| 523 | Colin MacDonald Alternative School | Hamilton | Site based only | No Association Membership | Visit |
| 652 | Greenhill Islamic School | Hamilton | Site based only | No Association Membership | — |
| 661 | Hamilton Downtown Islamic School | Hamilton | Site based only | No Association Membership | Visit |
| 662 | Hamilton Hebrew Academy Zichron Meir | Hamilton | Site based only | No Association Membership | Visit |
| 720 | Islamic School of Hamilton | Hamilton | Site based only | Other | Visit |
| 740 | Kehila Jewish Community Day School | Hamilton | Site based only | No Association Membership | Visit |
| 786 | Living Hope Christian School | Hamilton | Site based only | No Association Membership | Visit |