Flagler Estates is an unincorporated community and census-designated place (CDP) in St. Johns County in the U.S. state of Florida.

It is located 8 mi (13 km) southeast of Hastings is bordered by Flagler County to the south.

The Flagler Estates CDP encompasses a total of 11.94 sq mi (30.9 km2), 0.87% of which is covered in water, in unincorporated areas of St. Johns County.

Although Flagler Estates cover a wide area, the nearest services are in Palatka, across the St. Johns River.

2.4 miles (3.9 km) east of the area is Old Brick Road, a U.S. National Register of Historic Place.

In the 2006 codification bill, lands owned by FERWCD north of the Ashley Outfall were added into the District.