| St Anthony School | 0.0 |
Regular elementary or secondary | Pre-KG-8 | 115 | 17.4 | Roman Catholic |
| King's Christian Academy | 0.4 |
Regular elementary or secondary | 2-6 | 8 | 5.0 | Christian (no specific denomination) |
| St Luke's Episcopal School | 7.9 |
Regular elementary or secondary | Pre-KG-5 | 66 | 12.2 | Episcopal |
| Merced Montessori School | 8.1 |
Montessori | Pre-KG-KG | 5 | 3.1 | Nonsectarian |
| Merced Christian School | 8.3 |
Regular elementary or secondary | Pre-KG-8 | 147 | 11.8 | Christian (no specific denomination) |
| Alexander Street Montessori School | 8.5 |
Montessori | Pre-KG-KG | 5 | 2.6 | Nonsectarian |
| Our Lady Of Mercy School | 9.3 |
Regular elementary or secondary | Pre-KG-8 | 342 | 20.6 | Roman Catholic |
| Merced Adventist School | 9.7 |
Regular elementary or secondary | 1-8 | 14 | 7.0 | Seventh-Day Adventist |
| St Paul Lutheran | 9.8 |
Regular elementary or secondary | Pre-KG-5 | 92 | 15.3 | Lutheran Church - Missouri Synod |
| Valley Oaks School | 15.7 |
Special education | 6-8 | 15 | 7.5 | Nonsectarian |
| Sacred Heart School | 15.8 |
Regular elementary or secondary | KG-8 | 247 | 17.0 | Roman Catholic |
| Hughson Christian School | 22.4 |
Regular elementary or secondary | Pre-KG-8 | 27 | 8.2 | Church of Christ |
| Our Lady Of Miracles Catholic School | 22.7 |
Regular elementary or secondary | KG-8 | 166 | 16.6 | Roman Catholic |
| Los Banos Adventist School | 23.3 |
Regular elementary or secondary | Pre-KG-8 | 45 | 9.2 | Seventh-Day Adventist |
| Our Lady Of Fatima School | 24.7 |
Regular elementary or secondary | Pre-KG-8 | 190 | 19.4 | Roman Catholic |
