It is the only high school in the Allamakee Community School District and serves many of the surrounding towns, including: Harpers Ferry, Waterville, and Dorchester.

In 2007, a brand new $16 million addition was built onto the Senior High building.

Waukon Wellness Center was also built and opened across the street from the school.

Matt Hoover, season two winner of NBC's The Biggest Loser, spoke at the grand opening.

The athletic teams of Waukon High School are known as the Indians.