K-12 education for the City of Cotati is provided by the Cotati-Rohnert Park Unified School District. The school district is made up of 9 elementary schools (K-5), 2 middle schools (6-8) and 3 high schools (9-12). The main high school is Rancho Cotate High School, located just over the city limits in nearby Rohnert Park.

The City of Cotati is also fortunate to enjoy close proximity to two fine institutions of higher education. Sonoma State University, part of the California State University system, is located just one mile away and gives Cotati outstanding educational and cultural advantages. Just a few exits to the north on US 101 is the highly acclaimed Santa Rosa Junior College, offering a diverse array of certificate and degree programs.