The club's reserve team for the most part of its history played in the lower amateur leagues. It made a three-season appearance in the tier four Verbandsliga Südbaden from 1983 to 1986, with a third place in 1985 as its best result, but then took until 1994 to return to this league. In 1998 the team won promotion to the Oberliga Baden-Württemberg after a league championship in the Verbandsliga.
SC Freiburg II spent the next ten seasons at this level as an upper table side, never finishing outside the top seven, before another league championship in 1998 took the team to the Regionalliga Süd. After four seasons at this league the team became part of the new Regionalliga Südwest in 2012. After a seventh place in its first season in the league the team finished runner-up in 2013–14 but declined the right to take part in the promotion round to the 3. Liga and instead remained in the Regionalliga. At the end of the 2015–16 season Freiburg was relegated back to the Oberliga.
With the introduction of the Regionalligas in 1994 and the 3. Liga in 2008 as the new third tier, below the 2. Bundesliga, all leagues below dropped one tier. In 2012, the number of Regionalligas was increased from three to five with all Regionalliga Süd clubs except the Bavarian ones entering the new Regionalliga Südwest.