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For the 2025-26 school year, there are 3 public schools serving 312 students in Canistota, SD.

The top-ranked public schools in Canistota, SD are Canistota Elementary - 02, Canistota Middle School - 03 and Canistota High School - 01. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Canistota, SD public schools have an average math proficiency score of 57% (versus the South Dakota public school average of 43%), and reading proficiency score of 62% (versus the 51% statewide average). Schools in Canistota have an average ranking of 9/10, which is in the top 20% of South Dakota public schools.

Minority enrollment is 11% of the student body (majority American Indian), which is less than the South Dakota public school average of 33% (majority American Indian).