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For the 2025-26 school year, there are 5 public schools serving 1,475 students in Cheboygan, MI (there are , serving 164 private students). 90% of all K-12 students in Cheboygan, MI are educated in public schools (compared to the MI state average of 90%).

The top ranked public schools in Cheboygan, MI are Cheboygan Intermediate School, Cheboygan Middle School and Cheboygan Area High School. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Cheboygan, MI public schools have an average math proficiency score of 37% (versus the Michigan public school average of 35%), and reading proficiency score of 48% (versus the 46% statewide average). Schools in Cheboygan have an average ranking of 7/10, which is in the top 50% of Michigan public schools.

Minority enrollment is 17% of the student body (majority American Indian and Hispanic), which is less than the Michigan public school average of 37% (majority Black).