In 2013, the club was given the rights to a National Premier Soccer League franchise for Palm Beach County, Florida.

The initial plans for the team fell through at the last minute and the NPSL franchise was put on hiatus for two years.

APSL awarded Boca Raton a franchise and the club was officially announced on January 20, 2015.

Boca Raton went on a 9-game win streak to take both the 2015 APSL regular season title and championship.

After a year-long break in 2020 due to COVID-19, Boca Raton FC started competing again in the FGCL and the PASL in 2021, with participation confirmed for the NPSL season as well.