Flagler County Schools serves roughly 13,500 students across Palm Coast, Bunnell, and Flagler Beach, and is the county's largest employer with more than 2,000 staff. For families moving to the area, the district runs five elementary schools — Belle Terre, Bunnell, Lewis E. Wadsworth, Old Kings, and Rymfire — all serving grades PreK through 5. Middle school students attend Buddy Taylor Middle School or Indian Trails Middle School (grades 6–8), and the county's two high schools are Flagler-Palm Coast High School, home of the Bulldogs, and Matanzas High School, home of the Pirates. Both are Five-Star School Award recipients; Matanzas earned an "A" rating from the Florida Department of Education in 2024, and Flagler-Palm Coast offers an International Baccalaureate diploma program, the i3 New Tech Academy, and an Aeronautical Academy with Embry-Riddle dual-enrollment credit. Beyond the traditional public schools, families can choose Imagine School at Town Center (a K–8 public charter), iFlagler Virtual School for full- or part-time online learning, and Flagler Technical College for career and workforce training. Flagler County is also home to several private schools, including First Baptist Christian Academy, Freedomschoolers Academy, St. Elizabeth Ann Seton Catholic School, and Christ the King Lutheran School.

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