SV Jena joined the Gauliga Mitte, one of 16 top-flight divisions formed in the reorganization of German football under the Third Reich.

After the 1943–44 season, the Gauliga Mitte broke up into a collection of city-based leagues as World War II overtook the area.

In the immediate aftermath of the war, associations of all types (including sports and football clubs) were banned in Germany by the occupying Allied authorities.

In the aftermath of World War II, East Germany authorities tagged sports teams with the names of socialist heroes: Ernst Abbe was a local son and physicist associated with the Zeiss optical factory.

He made an early contribution to easing the plight of workers by introducing the 8-hour work day at the Zeiss plant, a milestone for labour during the late 19th century.

Since 1999 the team has primarily played tier III and IV football,[1] but a second place-finish in the Regionalliga Nord secured Jena promotion to the 2.

CZ Jena won the first match in Köln 3–2 and lost the second leg 1–0 at home, but were promoted on the away goals rule.

[10] As with Carl Zeiss Jena, Newport County have seen similar struggles off and on the pitch, and the teams regularly play each other during pre-season.

The club compete in a Thuringia derby with Rot-Weiß Erfurt, which often features violence between the two sets of supporters and use of pyrotechnics.

Before the end of World War II, Jena sent three players to the Germany national side: Willy Krauß (1911–12), Heinz Werner (1935) and Ludwig Gärtner (1939–41).

American defender, Brian Bliss, played at the club from 1992 to 1996 and received regular calls to the United States men's national soccer team.

He went on to play for MLS side Columbus Crew SC and would later serve as technical director in the club's front office.

The club's reserve team, FC Carl Zeiss Jena II, currently plays in the tier five NOFV-Oberliga Süd.