| Berean Baptist Christian Academy | 1.1 |
Regular elementary or secondary | Pre-KG-12 | 52 | 8.2 | Baptist |
| Santa Rosa Christian School | 6.9 |
Regular elementary or secondary | KG-12 | 203 | 9.7 | Christian (no specific denomination) |
| Stuart Preparatory School | 7.3 |
Special program emphasis | KG-9 | 40 | 10.0 | Nonsectarian |
| Paideia Educational Heritage | 7.9 |
Regular elementary or secondary | Pre-KG-12 | 12 | 6.0 | Christian (no specific denomination) |
| Montessori Schools Of Petaluma | 8.9 |
Montessori | Ungraded-Ungraded | 65 | 13.0 | Nonsectarian |
| Summerfield Waldorf School | 9.1 |
Special program emphasis | Pre-KG-12 | 344 | 8.0 | Nonsectarian |
| Anova Center For Education | 9.2 |
Special education | 1-12 | 53 | 10.6 | Nonsectarian |
| North Valley School | 9.3 |
Special education | 4-12 | 65 | 8.1 | Nonsectarian |
| Greenacre Homes Inc | 9.5 |
Special education | 5-12 | 47 | 15.7 | Nonsectarian |
| Lattice Educational Services | 9.7 |
Special education | Ungraded-Ungraded | 30 | 7.5 | Nonsectarian |
| Rincon Valley Christian School | 10.3 |
Regular elementary or secondary | Pre-KG-12 | 298 | 10.5 | Christian (no specific denomination) |
| Plumfield Academy | 10.5 |
Special education | 2-12 | 27 | 6.8 | Nonsectarian |
| Pacific Christian Academy | 10.9 |
Regular elementary or secondary | Pre-KG-12 | 33 | 4.7 | Church of Christ |
| Redwood Adventist Academy | 11.6 |
Regular elementary or secondary | Pre-KG-12 | 131 | 12.6 | Seventh-Day Adventist |
| Nonesuch School | 13.2 |
Alternative/other | Ungraded-Ungraded | 40 | 6.7 | Nonsectarian |
| American Christian Academy Ext | 13.9 |
Regular elementary or secondary | 1-12 | 47 | 9.4 | Nonsectarian |
| Sonoma Valley Academy | 14.2 |
Regular elementary or secondary | 6-12 | 19 | 4.4 | Nonsectarian |
| North Bay Christian Academy | 18.4 |
Regular elementary or secondary | KG-12 | 84 | 9.8 | Christian (no specific denomination) |
| Harvest Christian Academy | 19.3 |
Alternative/other | 1-12 | 159 | 6.3 | Christian (no specific denomination) |
| Hopewell Baptist Christian Academy | 20.9 |
Regular elementary or secondary | KG-12 | 61 | 12.2 | Baptist |
| Trinity Grammar And Prep | 21.5 |
Regular elementary or secondary | KG-12 | 93 | 10.9 | Roman Catholic |
| Aldea School | 21.6 |
Special education | 6-11 | 9 | 9.0 | Nonsectarian |
| Kolbe Academy | 22.4 |
Regular elementary or secondary | 1-11 | 34 | 6.8 | Roman Catholic |
| Napa Christian Campus Of Education | 22.4 |
Regular elementary or secondary | KG-12 | 191 | 11.7 | Seventh-Day Adventist |
| San Domenico School | 23.3 |
Regular elementary or secondary | KG-12 | 533 | 8.1 | Roman Catholic |
| Mulberry Classroom | 23.6 |
Special education | KG-11 | 18 | 3.5 | Nonsectarian |
