Affiliated to the multiple regional clubs, they currently only feature youth teams.

Until 2020, FC Sønderborg had a first team led by manager Kim Poulsen,[1] but the team withdrew from competition citing too little interest from parent clubs in providing senior players.

[3] In February 2009, FC Sønderborg was founded through a merger of 11 regional teams in order to create an elite youth academy for the under-13 to under-19 talents in Sønderborg Municipality.

In the fall of 2019, with FC Sønderborg facing relegation from the fifth-tier Jutland Series, manager Kim Poulsen criticised the historical lack of ambition in Sønderborg in creating an environment for divisional football.

[5] The first team withdrew from competition in April 2020, citing lacking interest from parent clubs in providing senior players.