The club was founded on 13 November 1930 and was made up largely of employees from the local chemical factory Wacker Chemie, which was established in 1914, and still sponsors the club today. The first football side in the city was part of the gymnastics club Turnverein Burghausen. In 1922, the footballers left TV to form 1. FC Burghausen which became part of SV at the time of its founding. Besides football, the new club had departments for shooting, athletics, and youth.
SV won the East Bavarian championship just three years later in 1933, but then afterwards toiled in anonymity in the local lower level leagues until 1993 when they won the Landesliga Bayern-Süd (V) title, followed by the Bayernliga (IV) championship two years later, which advanced the club to the Regionalliga Süd (III). In 2002–03, the team played its way into the Second Bundesliga where they competed until being relegated at the end of the 2006–07 campaign.
Wacker earned a seventh place finish in the Regionalliga in 2007–08, which qualified the team for the new 3rd Liga the following season. It finished the 2008–09 season in 18th place, on a relegation rank but was saved from having to step down to the Regionalliga by the withdrawal from the league of Kickers Emden for financial reasons.
The club finished in 18th place,on a relegation rank but was saved from having step down to the Regionalliga for second time by the insolvency of Rot Weiss Ahlen.
The SV Wacker Burghausen II team played in the Bayernliga (IV) from 2005 to 2007, making Burghausen one of the few clubs to have had both first and second teams play at this level. The reserve team finished 15th in the Landesliga Bayern-Süd (VI) in the 2010–11 season, narrowly avoiding relegation. At the end of the 2011-12 season the team qualified directly for the newly expanded Bayernliga after winning the league championship in the Landesliga.