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For the 2026 school year, there are 7 public schools serving 2,198 students in Houston, MS (there are , serving 17 private students). 99% of all K-12 students in Houston, MS are educated in public schools (compared to the MS state average of 89%).

The top-ranked public schools in Houston, MS are Houston High School, Houston Middle School and Houston Upper Elementary School. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Houston, MS public schools have an average math proficiency score of 61% (versus the Mississippi public school average of 53%), and reading proficiency score of 41% (versus the 42% statewide average). Schools in Houston have an average ranking of 7/10, which is in the top 50% of Mississippi public schools.

Minority enrollment is 51% of the student body (majority Black), which is less than the Mississippi public school average of 58% (majority Black).