Okaloosa County School Board
In 1994, Gaetz ran for the Okaloosa County School Board, receiving the Republican nomination and then challenging incumbent school board member Jean Long, the Democratic nominee, and Susan Matuska, the Libertarian nominee, in the general election. He ended up winning, receiving 69% of the vote to Long's 20% and Matuska's 11%.
During his first term, Gaetz campaigned for a one-cent sales tax to fund school construction and renovation, which was easily approved by the county's voters in a 1995 special election.
In 1997, he called for an investigation into the conduct of a vice-principal at Niceville High School, where his son went to school, after reports surfaced of the vice-principal promoting his religious beliefs while working at the school. Following his call for an investigation, which he said was warranted by the vice-principal's attempts "to make people who didn't share his views feel as though they were somehow second-class Christians or that they were in danger of damnation," he said, "I have received death threats from individuals who mistakenly believe the way to advance their own particular brand of Christianity is to threaten the life of someone who is a Christian not of their particular kind."
When he ran for re-election in 1998, Gaetz was opposed by only Republican candidate James Campbell, whom he defeated in an open primary with 67% of the vote.
Gaetz opted to run for Okaloosa County superintendent of schools in 2000, and faced David Morgan, the principal of Niceville High School, in the Republican primary. He defeated Morgan handily, winning 68% of the vote and advancing to the general election, where he was opposed by William Lynch, the Democratic nominee, and John Hughes, an independent candidate. Neither Lynch nor Hughes posed a significant challenge to Gaetz, and he won his first term with 75% of the vote to Lynch's 18% and Hughes' 7%. He was unopposed for re-election in 2004. During his time as superintendent, the Okaloosa County School District increased from twenty-seventh in the state in student performance to first.