| School Name | Grades | Address | Zip | Phone | County | Type | District Name |
| BASIS Flagstaff | 5-12 | 1700 N. Gemini Drive
Flagstaff, AZ | 86001 | (928) 774-5502 | Coconino | charter | |
| Carden of the Peaks | K-6 | 7680 E Gemini Drive
Flagstaff, AZ | 86004 | (928) 526-2789 | Coconino | private | |
| Charles W Sechrist Elementary School | K-5 | 2230 Fort Valley Rd.
Flagstaff, AZ | 86001 | (928) 773-4020 | Coconino | public | Flagstaff Unified District |
| Coconino High School | 9-12 | 2801 N Izabel Street
Flagstaff, AZ | 86004 | (928) 773-8200 | Coconino | public | Flagstaff Unified District |
| Eva Marshall Elementary School | K-5 | 850 N. Bonito St.
Flagstaff, AZ | 86001 | (928) 773-4030 | Coconino | public | Flagstaff Unified District |
| Excel Education Centers - Flagstaff | 9-12 | 2229 E. Spruce Ave.
Flagstaff, AZ | 86004 | (928) 214-7442 | Coconino | charter | |
| Flagstaff Arts and Leadership Academy | 7-12 | 3401 N. Fort Valley Rd.
Flagstaff, AZ | 86001 | (928) 779-7223 | Coconino | charter | |
| Flagstaff Community Christian School | K-8 | P.O. Box 30841
Flagstaff, AZ | 86003 | (928) 522-5968 | Coconino | private | |
| Flagstaff High School | 9-12 | 400 W Elm Street
Flagstaff, AZ | 86001 | (928) 773-8100 | Coconino | public | Flagstaff Unified District |
| Flagstaff Junior Academy | K-8 | 306 W. Cedar Avenue
Flagstaff, AZ | 86001 | (928) 774-6007 | Coconino | charter | |
| Haven Montessori Charter School | K | 2677 East 7th Avenue
Flagstaff, AZ | 86004 | (928) 522-0985 | Coconino | charter | |
| John Q Thomas Elementary School | K-5 | 3330 E. Lockett Rd.
Flagstaff, AZ | 86004 | (928) 773-4110 | Coconino | public | Flagstaff Unified District |
| Leupp Public School | K-8 | 3285 E. Sparrow Ave
Flagstaff, AZ | 86004 | (928) 686-6266 | Coconino | public | Flagstaff Unified District |
| Lura Kinsey Elementary School | K-5 | 1601 S. Lonetree Rd.
Flagstaff, AZ | 86001 | (928) 773-4060 | Coconino | public | Flagstaff Unified District |
| Manuel De Miguel Elementary School | K-5 | 3500 S Gillenwater Dr
Flagstaff, AZ | 86001 | (928) 773-4000 | Coconino | public | Flagstaff Unified District |
| Montessori Charter School of Flagstaff - Campus | K-8 | 850 N. Locust
Flagstaff, AZ | 86001 | (928) 226-1212 | Coconino | charter | |
| Mount Calvary Lutheran School | PK-6, 8 | 2605 N Fort Valley Rd
Flagstaff, AZ | 86001 | (928) 774-8811 | Coconino | private | |
| Mount Elden Middle School | 6-8 | 3223 N 4th Street
Flagstaff, AZ | 86004 | (928) 773-8250 | Coconino | public | Flagstaff Unified District |
| Mountain English Spanish Academy of Flagstaff (M.E.S.A.) | 6-8 | 2300 East 6th Avenue
Flagstaff, AZ | 86004 | (928) 773-4081 | Coconino | charter | |
| Mountain School | K-6 | 311 W Cattle Drive Trail
Flagstaff, AZ | 86001 | (928) 779-2392 | Coconino | charter | |
| Northland Preparatory Academy | 7-12 | 3300 W. Sparrow Ave.
Flagstaff, AZ | 86004 | (928) 214-8776 | Coconino | charter | |
| Pine Forest School | K-8 | 1120 West Kaibab Lane
Flagstaff, AZ | 86001 | (928) 779-9880 | Coconino | charter | |
| Ponderosa High School | 9-12 | 2384 N. Steves Blvd.
Flagstaff, AZ | 86004 | (928) 779-6884 | Coconino | public | Coconino County Regional Accommodation School District |
| Project New Start | 7-12 | 320 N Aztec
Flagstaff, AZ | 86001 | (928) 773-8198 | Coconino | public | Flagstaff Unified District |
| San Francisco De Asis | PK-8 | 320 N Humphreys St
Flagstaff, AZ | 86001 | (928) 779-1337 | Coconino | private | |
| Sinagua Middle School | 6-8 | 3950 E Butler Ave
Flagstaff, AZ | 86004 | (928) 527-5500 | Coconino | public | Flagstaff Unified District |
| Star Charter School | K-8 | 145 Leupp Road
Flagstaff, AZ | 86004 | (928) 606-7419 | Coconino | charter | |
| Sturgeon Cromer Elementary School | K-5 | 7150 E Silver Saddle Road
Flagstaff, AZ | 86004 | (928) 773-4150 | Coconino | public | Flagstaff Unified District |
| The Peak School | K-8 | 2016 North First Street A & B
Flagstaff, AZ | 86004 | (928) 779-0771 | Coconino | charter | |
| Thomas M Knoles Elementary School | K-5 | 4005 E Butler
Flagstaff, AZ | 86004 | (928) 773-4120 | Coconino | public | Flagstaff Unified District |
| W F Killip Elementary School | K-5 | 2300 E 6th Ave
Flagstaff, AZ | 86004 | (928) 773-4080 | Coconino | public | Flagstaff Unified District |
| Weitzel's Puente De Hozho Bilingual Magnet School | K-7 | 3401 N. Fourth Street
Flagstaff, AZ | 86004 | (928) 527-6108 | Coconino | public | Flagstaff Unified District |
