Onalaska is served by two school districts, Onalaska and Holmen.
Onalaska School District schools include Onalaska High School, Onalaska Middle School, Eagle Bluff Elementary School, Northern Hills Elementary School and Irving Pertzsch Elementary School.

Parochial schools in the city include Luther High School, a Lutheran high school of the Wisconsin Evangelical Lutheran Synod, St. Patrick Elementary School, part of La Crosse Aquinas Catholic Schools, and St. Pauls Lutheran School, serving grades pre-K through 8.
Onalaska is served by two school districts, Onalaska and Holmen. Onalaska School District schools include Onalaska High School, Onalaska Middle School, Eagle Bluff Elementary School, Northern Hills Elementary School and Irving Pertzsch Elementary School.
Parochial schools in the city include Luther High School, a Lutheran high school of the Wisconsin Evangelical Lutheran Synod, St. Patrick Elementary School, part of La Crosse Aquinas Catholic Schools, and St. Pauls Lutheran School, serving grades pre-K through 8.
Onalaska, Wisconsin