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For the 2025-26 school year, there is 1 public middle school serving 67 students in Canistota, SD.

The top-ranked public middle school in Canistota, SD is Canistota Middle School - 03. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Canistota, SD public middle school have an average math proficiency score of 47% (versus the South Dakota public middle school average of 39%), and reading proficiency score of 57% (versus the 49% statewide average). Middle schools in Canistota have an average ranking of 8/10, which is in the top 30% of South Dakota public middle schools.

Minority enrollment is 10% of the student body (majority American Indian), which is less than the South Dakota public middle school average of 42% (majority American Indian).