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For the 2025-26 school year, there are 2 private schools serving 190 students in Hillsboro, MO (there are , serving 6,521 public students). 3% of all K-12 students in Hillsboro, MO are educated in private schools (compared to the MO state average of 12%).

100% of private schools in Hillsboro, MO are religiously affiliated (most commonly Catholic and Christian).