| 1 | Flagstaff High SchoolFLAGSTAFF | High | 1,625 |
| 2 | Coconino High SchoolFLAGSTAFF | High | 1,506 |
| 3 | Sinagua Middle SchoolFLAGSTAFF | Middle | 1,035 |
| 4 | Mount Elden Middle SchoolFLAGSTAFF | Middle | 677 |
| 5 | Manuel DeMiguel Elementary SchoolFLAGSTAFF | Primary | 559 |
| 6 | Weitzel's Puente de Hozho Bilingual Magnet SchoolFLAGSTAFF | Primary | 430 |
| 7 | Charles W Sechrist Elementary SchoolFLAGSTAFF | Primary | 429 |
| 8 | Thomas M Knoles Elementary SchoolFLAGSTAFF | Primary | 428 |
| 9 | W F Killip Elementary SchoolFLAGSTAFF | Primary | 392 |
| 10 | Eva Marshall Elementary SchoolFLAGSTAFF | Primary | 384 |
| 11 | Sturgeon Cromer Elementary SchoolFLAGSTAFF | Primary | 378 |
| 12 | John Q Thomas Elementary SchoolFLAGSTAFF | Primary | 369 |
| 13 | Lura Kinsey Elementary SchoolFLAGSTAFF | Primary | 343 |
| 14 | Leupp Public SchoolFLAGSTAFF | Primary | 148 |
| 15 | Summit High SchoolFLAGSTAFF | High | 95 |
| 16 | Northern Arizona Distance LearningFLAGSTAFF | High | 22 |
| 17 | Flagstaff Middle School - ClosedFLAGSTAFF | -- | 0 |
| 18 | Continental ProjectFLAGSTAFF | -- | 0 |
| 19 | Neil V Christensen School - ClosedFLAGSTAFF | -- | 0 |
| 20 | Renaissance Magnet Middle School - ClosedFLAGSTAFF | -- | 0 |
| 21 | Sinagua High School - ClosedFLAGSTAFF | -- | 0 |
| 22 | South Beaver Elementary School - ClosedFLAGSTAFF | -- | 0 |