In the village, 93.2% of the population 25 years and older hold a high school diploma or higher, 43.5% a bachelor's degree or higher, and 16.4% a graduate/professional degree.

Public schools in Honeoye Falls are part of the Honeoye Falls-Lima Central School District. Schools within the village include Honeoye Falls-Lima Senior High School, Honeoye Falls-Lima Middle School, and Manor Intermediate School. The Lima Primary School is in the district but located in Town of Lima. The School mascot is the Cougar.