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For the 2025-26 school year, there are 11 public schools serving 4,700 students in Brookhaven, MS (there are , serving 904 private students). 84% of all K-12 students in Brookhaven, MS are educated in public schools (compared to the MS state average of 89%).

The top ranked public schools in Brookhaven, MS are West Lincoln School, Middle School For The Arts and Enterprise School. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Brookhaven, MS public schools have an average math proficiency score of 46% (versus the Mississippi public school average of 53%), and reading proficiency score of 40% (versus the 42% statewide average). Schools in Brookhaven have an average ranking of 5/10, which is in the bottom 50% of Mississippi public schools.

Minority enrollment is 46% of the student body (majority Black), which is less than the Mississippi public school average of 58% (majority Black).