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For the 2025-26 school year, there are 2 public schools serving 638 students in Winnebago, NE (there are , serving 100 private students). 86% of all K-12 students in Winnebago, NE are educated in public schools (compared to the NE state average of 89%).

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

Winnebago, NE public schools have an average math proficiency score of 21% (versus the Nebraska public school average of 58%), and reading proficiency score of 14% (versus the 47% statewide average). Schools in Winnebago have an average ranking of 1/10, which is in the bottom 50% of Nebraska public schools.

Minority enrollment is 100% of the student body (majority American Indian), which is more than the Nebraska public school average of 38% (majority Hispanic).