Flagler County is governed by five elected Commissioners, each representing one of five geographic districts. Commissioners are elected at-large and serve four-year staggered terms. Districts 1, 3, and 5 are up for election in presidential years; Districts 2 and 4 in midterm years.

Administrative departments operate under the County Administrator per Florida Statute §125.70–125.74. Constitutional officers are independently elected and operate separately from the Board of County Commissioners.