The club was founded in May 1903 by workers at the Carl Zeiss AG optics factory as the company-sponsored Fussball-Club der Firma Carl Zeiss. The club underwent name changes in 1911 to Fussball Club Carl Zeiss Jena e.V. and in March 1917 to 1. Sportverein Jena e.V.
In 1933, 1. SV Jena joined the Gauliga Mitte, one of 16 top-flight divisions formed in the reorganization of German football under the Third Reich. The team captured division titles in 1935, 1936, 1940, and 1941. This earned Jena entry to the national finals, but they performed poorly and were never able to advance out of preliminary-round group play. 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. Jena was reconstituted in June 1946 as SG Ernst Abbe Jena and, like many other clubs in East Germany, would undergo a number of name changes: SG Stadion Jena (October 1948), SG Carl Zeiss Jena (March 1949), BSG Mechanik Jena (January 1951), BSG Motor Jena (May 1951) and SC Motor Jena (November 1954).
In the aftermath of World War II, East German 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).
In 1950 the club became a founding member of the DDR Liga (II), and in their second season captured a divisional title to win promotion to the top-flight DDR Oberliga for a single-season appearance. Renamed SC Motor Jena in 1954, they played their way back to the upper league by 1957. Jena won its first honours with the capture of the FDGB-Pokal in 1960 and followed up with the East German national title in 1963. The club was "re-founded" as FC Carl Zeiss Jena in January 1966, and became one of East Germany's football clubs, "focus centres" for the development of talented players for the national side. Jena would go on to become a dominant side in the DDR-Oberliga between then and 1975. They took two more national titles in 1968 and 1970, but finished in second place another half-dozen times to sides like Vorwärts Berlin, Dynamo Dresden and 1. FC Magdeburg. In addition to their national titles, FCC captured East German Cups in 1972, 1974 and 1980. The club also appeared in the 1981 European Cup Winners' Cup final, losing 1–2 to Dinamo Tbilisi. This was arguably the club's greatest achievement.
After German reunification in 1990, Jena was seeded into the 2. Bundesliga. Their second-place finish in 1992 deteriorated into a 17th-place finish in 1994 and relegation to Regionalliga Nordost (III). They won immediate re-promotion, and played for three more years at the tier-II level. Since 1999 the team has primarily played tier III and IV football, but a second place-finish in the Regionalliga Nord secured Jena promotion to the 2. Bundesliga for the 2006–07 season. Jena remained in the 2. Bundesliga in 2007–08, avoiding relegation by winning 2–1 away against FC Augsburg in their final match of the season. They would finish last in the 2. Bundesliga in 2007–08, returning to the third tier. However, this would not be one of the Regionalligen; the German Football Association (DFB) launched the new 3. Liga for 2008–09, of which Jena was a charter member. On 9 November 2009 Chairman Peter Schreiber announced his retirement; on 13 November the executive board accepted his resignation, and on 25 November Hartmut Bayer became the new chairman. The second team was involved in the 2009 European football betting scandal, accused of match-fixing in the game against ZFC Meuselwitz. On 10 December 2009 the club announced that it was in financial distress, owing over €1 million. In January 2010 the players agreed to accept a lower salary.
The club was relegated from the 3. Liga in 2012 at has been playing in the tier four Regionalliga Nordost as an upper table side, finishing second in 2013 and third in 2014.
^The Gauliga Mitte was the highest football league in the Prussian province of Saxony and the German states of Thuringia and Anhalt from 1933 to 1945. It was also the highest top tier of German football during this time, along with 15 other regions of the Gauliga.
^The Regionalliga Nordost was the third tier of the German football league system in the states of the former East Germany and West Berlin.
The club's reserve team, FC Carl Zeiss Jena II, currently plays in the tier five NOFV-Oberliga Süd. It first played at this level from 1994 to 1999, and again since 2006 with a third place in 1996 and 2010 as its best results.