The club was founded on 5 May 1905 and played in the local leagues. The team attempted a merger with Turngemeinde Schweinfurt von 1848 which lasted from 1928 to 1930 before the two groups parted ways again and the football division became 1. Fussball-Club Schweinfurt 1905 VfL. While the club did not reap the expected benefits from the brief union, it improved dramatically after re-establishing itself as an independent club. Membership grew significantly and a number of new sports departments were formed within the organization.
Schweinfurt finally gained first class status with its entry into the Bezirksliga Bayern in 1931. The club had a couple of successful seasons in the Gauliga era, winning the Gauliga Bayern in 1939 and 1942 and qualifying for the German championship round.
After the 2nd World War, the club was integrated into the Oberliga Süd where it played for the duration of the league's existence until the Bundesliga, Germany's new professional league, was founded in 1963. One year later it found itself playing in the second tier Regionalliga Süd. In 1966 the club made it to the Bundesliga advancement games but was unable to ascend to the top tier. With the introduction of the 2nd Bundesliga Süd in 1974, Schweinfurt qualified despite only finishing 15th in the last Regionalliga season.
After the 1976 season the club began to falter: poor results and financial problems saw the club descend first to the Amateurliga Bayern (III) and then, for the first time in 1984, to the Landesliga Bayern-Nord (IV). Schweinfurt became an "elevator club" ascending and descending between tiers III and IV, with just a pair of brief 2.Bundesliga appearances in 1990–91 and in 2001–02, the latter when the team's third place finish allowed it to pass the amateur division of VfB Stuttgart because that club was not eligible to advance a second team into the professional ranks.
Disasters happened in 2004 when then club was forced to leave the Regionalliga Süd (III) because of financial reasons and 2005 when the club went bankrupt and the team's results in the Oberliga Bayern (IV) were annulled. A re-structured club has since enjoyed some success, working its way back into the Oberliga Bayern (IV).
The club struggled from the start in its 2007–08 Oberliga Bayern season, but improved in the second half. In the end, a 16th place meant they had to go through a promotion round with the third-placed Landesliga teams. After a convincing first round win over DJK Vilzing (5–1), the final match was lost to TSV Rain am Lech, losing 0–3 after extra time. This result meant, the FCS would have had to return to the Landesliga for next season, but the refusal of a Regionalliga licence for the Sportfreunde Siegen and the promotion of the 1. FC Eintracht Bamberg in their stead meant, an additional Bayernliga spot was available, which went to the FCS.
FCS was relegated again to the Landesliga in 2009 but returned to the Bayernliga immediately the following year. At the end of the 2011–12 season the club managed to qualify for the promotion round to the new Regionalliga Bayern and advanced to the second round after defeating SV Schalding-Heining on away goals. In this round the club missed out on promotion to FC Augsburg II after a 3–0 loss at home in extra time, first having drawn the away leg nil all.
In the 2012-13 season the club took out the championship in the northern division of the Bayernliga and thereby earned direct promotion to the Regionalliga Bayern. The team struggled against relegation all season, in the end finishing on a relegation play-off rank courtesy to a controversial final game of the season where Schweinfurt turned a 1–3 deficit into a 4–3 win with three goals in the last four minutes of the game. Schweinfurt successfully defended its league place in the relegation round and will continue to play in the league in 2014–15.
With the introduction of the Bezirksoberligas in 1988 as the new fifth tier, below the Landesligas, all leagues below dropped one tier. 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. With the establishment of the Regionalliga Bayern as the new fourth tier in Bavaria in 2012 the Bayernliga was split into a northern and a southern division, the number of Landesligas expanded from three to five and the Bezirksoberligas abolished. All leagues from the Bezirksligas onwards were elevated one tier.
The club made a semi-final appearance in 1936, when it lost 3–2 to FC Schalke 04, the closest it ever came to winning a national title. All its other ventures in the national cup ended in the first or second round, except in 1989–90, when it lost to Eintracht Braunschweig in the third round.