| Our Redeemer Lutheran School | 6.6 |
Regular elementary or secondary | Pre-KG-6 | 60 | 7.7 | Lutheran Church - Missouri Synod |
| Raynor Country Day School | 7.5 |
Regular elementary or secondary | Pre-KG-6 | 97 | 3.4 | Nonsectarian |
| Our Lady Queen Of Apostles Reg Catholic School | 10.4 |
Regular elementary or secondary | Pre-KG-8 | 205 | 13.1 | Roman Catholic |
| Our Lady Of Mercy Regional School | 11.6 |
Regular elementary or secondary | Pre-KG-6 | 153 | 20.4 | Roman Catholic |
| Southampton Montessori School | 13.0 |
Montessori | Pre-KG-KG | 12 | 7.5 | Nonsectarian |
| Step By Step Early Learning Center | 15.1 |
Montessori | Pre-KG-Trans. KG | 11 | 5.5 | Nonsectarian |
| Our/lady Of The Hampstons | 15.1 |
Regular elementary or secondary | Pre-KG-8 | 285 | 13.2 | Roman Catholic |
| Ross School | 18.7 |
Regular elementary or secondary | Pre-KG-4 | 119 | 4.3 | Nonsectarian |
| Montessori School Of Selden | 18.8 |
Early childhood program/child care center | Pre-KG-KG | 7 | 7.0 | Nonsectarian |
| The Hayground School | 18.9 |
Alternative/other | Pre-KG-8 | 51 | 6.5 | Nonsectarian |
| North Shore Christian School | 19.4 |
Regular elementary or secondary | Pre-KG-8 | 108 | 5.7 | Baptist |
| Our Lady Of Wisdom Regional School | 20.3 |
Regular elementary or secondary | KG-8 | 219 | 15.8 | Roman Catholic |
| Emanuel Lutheran School | 20.6 |
Regular elementary or secondary | Pre-KG-8 | 113 | 8.5 | Lutheran Church - Missouri Synod |
| Stella Maris Regional School | 20.7 |
Regular elementary or secondary | Pre-KG-8 | 123 | 9.5 | Roman Catholic |
| Holy Angels Regional School | 21.0 |
Regular elementary or secondary | KG-8 | 385 | 16.8 | Roman Catholic |
| Kiddie Academy E Setauket | 21.5 |
Early childhood program/child care center | Pre-KG-KG | 14 | 14.0 | Nonsectarian |
| Maimonides Day School | 23.5 |
Regular elementary or secondary | Pre-KG-6 | 11 | 3.2 | Jewish |
| Kids Place Early Childhood Day School | 23.7 |
Montessori | Pre-KG-KG | 11 | 11.0 | Nonsectarian |
| St Joseph School | 24.2 |
Regular elementary or secondary | Pre-KG-8 | 186 | 12.5 | Roman Catholic |
| North Shore Montessori | 24.3 |
Montessori | Pre-KG-KG | 19 | 4.8 | Nonsectarian |
| Prince Of Peace Regional School | 24.7 |
Regular elementary or secondary | Pre-KG-8 | 172 | 11.6 | Roman Catholic |
| St Elizabeth | 24.8 |
Regular elementary or secondary | Pre-KG-8 | 212 | 19.6 | Roman Catholic |
