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For the 2025-26 school year, there are 2 public schools serving 156 students in Mercer, MO (there are , serving 12 private students). 93% of all K-12 students in Mercer, MO are educated in public schools (compared to the MO state average of 88%).

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

Mercer, MO public schools have an average math proficiency score of 36% (versus the Missouri public school average of 40%), and reading proficiency score of 56% (versus the 43% statewide average). Schools in Mercer have an average ranking of 8/10, which is in the top 30% of Missouri public schools.

Minority enrollment is 8% of the student body (majority American Indian), which is less than the Missouri public school average of 32% (majority Black).