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For the 2025 school year, there are 9 public schools serving 4,675 students in Junction City, KS (there are , serving 297 private students). 94% of all K-12 students in Junction City, KS are educated in public schools (compared to the KS state average of 92%).

The top ranked public schools in Junction City, KS are Sheridan Elementary School, Spring Valley Elementary School and Grandview Elementary School. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Junction City, KS public schools have an average math proficiency score of 31% (versus the Kansas public school average of 30%), and reading proficiency score of 31% (versus the 33% statewide average). Schools in Junction City have an average ranking of 6/10, which is in the top 50% of Kansas public schools.

Minority enrollment is 55% of the student body (majority Hispanic), which is more than the Kansas public school average of 39% (majority Hispanic).