Flagler College is a member of the Independent Colleges and Universities of Florida, Council on Independent Colleges, and the Florida Association of Colleges and Universities. The college now has an upper division program at Tallahassee Community College and a bachelor of science in public administration program in partnership with St. Johns Community College in St. Augustine.

Athletic membership is in the NAIA.

Flagler College is also closely affiliated with Communities in Schools, Gallaudet University, The St. Augustine Foundation Center for Historic Research and Young Life.

In addition, the College is involved in a collaborative project with the University of Florida, The Historic St. Augustine Research Institute, which has its office on the Flagler College campus.

The College also is a member of the St. Augustine and St. Johns County Chamber of Commerce.