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For the 2025-26 school year, there are 4 public schools serving 459 students in Pawnee County, NE (there are , serving 15 private students). 97% of all K-12 students in Pawnee County, NE are educated in public schools (compared to the NE state average of 89%).

The top ranked public schools in Pawnee County, NE are Lewiston High School, Pawnee City Elementary School and Pawnee City Secondary School. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Pawnee County, NE public schools have an average math proficiency score of 43% (versus the Nebraska public school average of 58%), and reading proficiency score of 33% (versus the 47% statewide average). Schools in Pawnee County have an average ranking of 1/10, which is in the bottom 50% of Nebraska public schools.

Minority enrollment is 5% of the student body (majority Black and Hispanic), which is less than the Nebraska public school average of 38% (majority Hispanic).