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For the 2025-26 school year, there are 2 public schools serving 3,017 students in Neptune Beach, FL (there are , serving 385 private students). 89% of all K-12 students in Neptune Beach, FL are educated in public schools (compared to the FL state average of 86%).

The top-ranked public schools in Neptune Beach, FL are Neptune Beach Elementary School and Duncan U. Fletcher High School. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Neptune Beach, FL public schools have an average math proficiency score of 59% (versus the Florida public school average of 52%), and reading proficiency score of 62% (versus the 52% statewide average). Schools in Neptune Beach have an average ranking of 8/10, which is in the top 30% of Florida public schools.

Minority enrollment is 33% of the student body (majority Hispanic and Black), which is less than the Florida public school average of 66% (majority Hispanic).