| Charles W Sechrist Elementary School | PK - 6 | 508 | 18.0 | 86001 |
| Eva Marshall Elementary School | K - 6 | 522 | 16.7 | 86001 |
| Flagstaff Junior Academy | K - 8 | 206 | | 86001 |
| John Q Thomas Elementary School | K - 6 | 497 | 16.5 | 86004 |
| Leupp Public School | K - 8 | 209 | 11.7 | 86004 |
| Lura Kinsey Elementary School | K - 6 | 448 | 16.3 | 86001 |
| Manuel Demiguel Elementary School | K - 6 | 616 | 10.8 | 86001 |
| Montessori Charter School Of Flagstaff - Campus | K - 8 | 259 | | 86001 |
| Mountain School | K - 6 | 137 | | 86001 |
| Neil V Christensen School | PK - 6 | 447 | 16.9 | 86004 |
| Pine Forest School | K - 8 | 210 | | 86001 |
| South Beaver Elementary School | K - 6 | 312 | 16.7 | 86001 |
| Star Charter School | K - 8 | 54 | | 86004 |
| Sturgeon Cromer Elementary School | PK - 6 | 598 | 18.0 | 86004 |
| The Peak School | K - 8 | 121 | | 86004 |
| Thomas M Knoles Elementary School | K - 6 | 667 | 19.1 | 86004 |
| Thomas R Weitzel Elementary School | K - 6 | 0 | | 86004 |
| W F Killip Elementary School | PK - 6 | 488 | 13.3 | 86004 |
| Weitzel'S Puente De Hozho Bilingual Magnet School | K - 6 | 446 | 16.1 | 86004 |
| Flagstaff Middle School | 7 - 8 | 744 | 16.8 | 86001 |
| Mount Elden Middle School | 7 - 8 | 784 | 14.5 | 86004 |
| Mountain English Spanish Academy Of Flagstaff (M.E | 6 - 8 | 43 | | 86004 |
| Renaissance Magnet Middle School | 7 - 8 | 79 | 14.4 | 86004 |
| Bright Angel High School | 9 - 12 | 0 | | 86001 |
| Coconino High School | 9 - 12 | 1,351 | 18.9 | 86004 |
| County Jail Education Program | 7 - 12 | 3 | 3.8 | 86001 |
| Excel Education Centers Flagstaff, Llc | 9 - 12 | 74 | | 86004 |
| Flagstaff Arts And Leadership Academy | 9 - 12 | 150 | | 86001 |
| Flagstaff High School | 9 - 12 | 1,426 | 19.8 | 86001 |
| Northland Preparatory Academy | 7 - 12 | 324 | | 86004 |
| Ponderosa High School | 9 - 12 | 53 | 18.9 | 86004 |
| Project New Start | 7 - 12 | 63 | 12.6 | 86001 |
| Sinagua High School | 9 - 12 | 1,017 | 17.7 | 86004 |
| Juvenile Detention Education Program | 4 - 12 | 13 | 13.0 | 86001 |
