Founded in 1907, the team has played for most of its history as an unknown local side, although they did manage three seasons in the Bezirksliga Bayern, from 1930 to 1933, and two single season appearances in the Gauliga Bayern (1940–41, 1942–43) one of sixteen top-flight division established in the re-organization of German football under the Third Reich.
The club became part of the Landesliga Bayern (II) after the Second World War. Kickers put on some strong performances through the 50s in the Amateurliga Bayern (II-III) but never quite managed a breakthrough. Through the 60s and on into the early 80s the club played as a third division side with the exception of a single season (1977–78) played in the 2. Bundesliga after their divisional title win in the Oberliga Bayern (III) in '77. By 1983 financial difficulties contributed to a slide to fourth division play in the Landesliga Bayern-Nord which became a fifth tier circuit in 1994. Two difficult seasons over 2002–2004 saw the club descend through the Bezirksoberliga Unterfranken (VI) to the Bezirksliga Unterfranken (VII). Kickers recovered and returned to the Oberliga Bayern on the strength of a 2nd place in the 2007–08 Landesliga season. The club met local rival Würzburger FV there for the first Würzburg league derby since 1998–99.
The 2008–09 season proved no success, with Kickers immediately relegated again to the Landesliga and taking until 2012 to win this league again. The team was one of two clubs in the league to apply for a licence in the new tier four Regionalliga Bayern. Taking part in the promotion play off, Kickers earned a by in the first round and defeated BC Aichach in the second to play in the Regionalliga from 2012. The club was thereby also able to win promotion from the sixth tier to the fourth without playing in the fifth.
Prior to 1967 the club used the Randersacker Straße stadium and since then have played in the Kickers-stadion Am Dallenberg which has a capacity of 14,500 (~4,000 seats). The facility was renovated in 2005.
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 2009–10 season was the 19th time, the two most prominent clubs from Würzburg played in the same league since 1963. In this time, the derby was played on professional level only once, in the 1977–78 2nd Bundesliga Süd season.