| School Name | Grades | Address | Zip | Phone | County | Type | District Name |
| Alexander Junior High School | 5-8 | 713 Beauregard St
Brookhaven, MS | 39601 | (601) 833-7549 | Lincoln | public | Brookhaven School District |
| Brookhaven Academy | PK-12 | P.O. Box 3339
Brookhaven, MS | 39603 | (601) 833-4041 | Lincoln | private | |
| Brookhaven Elementary School | 1-4 | 300 South Church St
Brookhaven, MS | 39601 | (601) 833-3139 | Lincoln | public | Brookhaven School District |
| Brookhaven High School | 9-12 | 443 East Monticello St
Brookhaven, MS | 39601 | (601) 833-4498 | Lincoln | public | Brookhaven School District |
| Brookhaven Technical Center | 9-12 | 325 East Court St
Brookhaven, MS | 39601 | (601) 833-8335 | Lincoln | public | Brookhaven School District |
| Enterprise School | PK-12 | 1601 Hwy 583 SE
Brookhaven, MS | 39601 | (601) 833-7284 | Lincoln | public | Lincoln County School District |
| Lipsey School | 3-6 | 412 Drury Ln
Brookhaven, MS | 39601 | (601) 833-6148 | Lincoln | public | Brookhaven School District |
| Loyd Star School | PK-12 | 1880 Hwy 550 NW
Brookhaven, MS | 39601 | (601) 833-3473 | Lincoln | public | Lincoln County School District |
| Mamie Martin Elementary School | PK-2 | 420 Vivian Merritt St
Brookhaven, MS | 39601 | (601) 833-7359 | Lincoln | public | Brookhaven School District |
| MS School for the Arts | 11-12 | 308 West Cherokee St
Brookhaven, MS | 39601 | (601) 823-1300 | Lincoln | public | Middle School for the Arts |
| Mullins School | 2-12 | 413 S. Hamilton Street
Brookhaven, MS | 39601 | (601) 833-7479 | Lincoln | public | Brookhaven School District |
| West Lincoln School | PK-12 | 948 Jackson Liberty Dr SW
Brookhaven, MS | 39601 | (601) 833-4600 | Lincoln | public | Lincoln County School District |
