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For the 2025-26 school year, there are 6 public schools serving 2,116 students in Waynesboro, MS (there are , serving 269 private students). 89% of all K-12 students in Waynesboro, MS are educated in public schools (compared to the MS state average of 89%).

The top ranked public schools in Waynesboro, MS are Wayne County High School, Beat Four Elementary School and Waynesboro Riverview Ele School. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Waynesboro, MS public schools have an average math proficiency score of 39% (versus the Mississippi public school average of 53%), and reading proficiency score of 30% (versus the 42% statewide average). Schools in Waynesboro have an average ranking of 4/10, which is in the bottom 50% of Mississippi public schools.

Minority enrollment is 70% of the student body (majority Black), which is more than the Mississippi public school average of 58% (majority Black).