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For the 2025-26 school year, there are 6 public schools serving 3,448 students in Port Jefferson Station, NY (there are , serving 10 private students). 100% of all K-12 students in Port Jefferson Station, NY are educated in public schools (compared to the NY state average of 85%).

The top ranked public schools in Port Jefferson Station, NY are Comsewogue High School, Boyle Road Elementary School and John F Kennedy Middle School. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Port Jefferson Station, NY public schools have an average math proficiency score of 45% (versus the New York public school average of 52%), and reading proficiency score of 47% (versus the 49% statewide average). Schools in Port Jefferson Station have an average ranking of 4/10, which is in the bottom 50% of New York public schools.

Minority enrollment is 47% of the student body (majority Hispanic), which is less than the New York public school average of 60% (majority Hispanic).