The reserve team of Jahn Regensburg first rose to prominence when it played at the highest Bavarian level, then the tier three Bayernliga, for a season in 1962–63, courtesy to a title in the 2nd Amateurliga Niederbayern in 1962.

With the decline of the senior team which was relegated from the tier two 2nd Oberliga Süd to the Bayernliga in 1963 the reserve side quickly disappeared into regional football again.

[1] The team returned to Bayernliga level in 2002 when it took up the spot of SG Post/Süd Regensburg in the league, the later having joined Jahn that year, now playing as Jahn Regensburg II as the senior team was not a professional side anymore.

[1] While the first team returned to the Regionalliga Süd immediately the following year Jahn II spend the next six seasons in the Landesliga.

In 2013 the side was then transferred to the northern division where it played for three seasons until 2016 when it moved back to the south.