Sen. Flake believes that education decisions are best handled primarily at the state and local levels. Sen. Flake opposes the continued federal expansion into the education system, where too many dollars end up being spent on layers of bureaucracy instead of on students. Instead, he would like state tax dollars to go directly to local schools without going through Washington first. He believes that Arizonans can best make decisions related to Arizona's educational needs.

He has opposed attempts to expand the federal government’s reach into education, including voting against the No Child Left Behind Act.  

A longtime proponent of school choice, Sen. Flake played a pivotal role in 2003 in creating a scholarship program for children in failing schools in Washington, D.C., where the federal government has jurisdiction over education.