Based in Coral Gables, FECI is the direct lineal descendant of the various companies founded by pioneering American businessman Henry M. Flagler.

Although Florida East Coast Railway at one time fell under the FECI umbrella, it is now a completely separate corporate entity owned by Grupo México's GMexico Transportes SAB de CV since 2017.

Although FECI did not exist as a corporate entity until 2006, the company's origins date back to December 31, 1888, when Henry Flagler purchased the Jacksonville, St. Augustine and Halifax River Railway.

Convinced of the region's tourism potential, Flagler began laying a network of tracks and depots further and further south, which helped spur the development of the entire east coast of Florida.

In 1904, Flagler began construction on the Oversea Railway to Key West, which many people thought was an impossible undertaking.

FECR declared bankruptcy and was placed into receivership in September 1931 following financial difficulties caused by the Stock Market Crash of 1929 and onset of the Great Depression.

Later in 1961, shortly after taking over, the FECR and all other American railroads were notified by their non-operating unions that they expected a substantial hourly increase to go into effect at the end of the year.

Foxx Holdings began operating separately from the St. Joe Company in 2000 and was renamed FECI in April 2006.