The club was founded by Albanian migrants in 1970 and originally played under the name 'South Dandenong'. Today, the remnants of the clubs original founders is still seen, with the club still backed by a large majority of Albanian-Australians living in Melbourne and an ever growing football-fan base derived from the local and surrounding suburbs. 'South Dandenong' started competing in the Victorian District League (East Division), which was the eighth tier of football in the Victorian Football Pyramid. For decades 'South Dandenong' played in the lower divisions until the mid 90's when the clubs competitiveness finally took off. In 1994 'South Dandenong' then playing in State League Division 3, managed to move up a tier every year following until they reached the Victorian Premier League in 1998.
1990s
After a successful 1997 season, 'South Dandenong' were crowned champions of Victorian State League (Division 1). 'South Dandenong' played their first ever Victorian Premier League season in 1998. Being led by their player-coach Fadil Muriqi, the team managed to stay in the Victorian Premier League after finishing the season in 12th place. In the following year (1999) The team was not so lucky, and failed to avoid relegation resulting in them being demoted back down to (State Division 1).
2000-present
'South Dandenong' won promotion again to the exclusive Victorian Premier League in 2001 but were relegated again as the season ended.
At the end of the season 'South Dandenong' was to be no more, and underwent a name change to the "Dandenong Thunder" we see alive and kicking today. Since 2001 "Dandenong Thunder" seemed happy to spend seven competitive years in (Division 1) before the club decided to make a push for a higher level of competition. In 2007 with hopes of reaching the pinnacle of state football again the club signed boom recruits Veton Korcari from Richmond SC as well as Louis Brain, a former player with Adelaide United in the A-League. Joe Di Iorio, Marcus Stergiopoulos, Alfonso Opazo and Levent Osman were other big names who put on the Thunder jersey for a successful 2009 season.
2008 - Dandenong Thunder S.C - Under New Management achieved its aim in getting promoted back into the Victorian Premier League after a 7 year absence. It finished second on the ladder, only 3 points behind eventual champions Sunshine Georgies. The season saw the Dandenong Thunder on an impressive 17 game unbeaten streak, which was the catalyst in gaining promotion.
2009 - Dandenong Thunder S.C - Aimed at setting a top 6 finish for the season in establish itself as one of the VPL's powerhouses of football; the Thunder exceeded all expectations in its return to top flight football in Victoria by claiming The Victorian Premier League Minor Premiership.
After a 7 year hiatus, The Thunder managed to prove all nay-sayers wrong by clinching the 2009 Minor Premiership after beating its nearest opponent on the ladder by a staggering 12 points. The season included going the first 15 rounds undefeated and set a club record 31 game undefeated streak (overall) after not losing a single game since round 5 of the previous 2008 season. The 2009 VPL season also saw individual honours to some of the Thunder stars. Dandenong youngster Jack Hingert was selected to play for new A-League side North Queensland Fury, whilst Joey Di Iorio claimed the golden boot for leading goal scorer in the league. Dandenong Thunder coach Stuart Munro was named Coach of the Year. In 2009, Thunder players, Hamlet Armenian, Ryan Davidson, Jack Hingert, Aron Wilford & Sam Bailey were also honorably selected to represent a super Victorian 11 which played a series of games against A-League champions Melbourne Victory.
2012 - 2012 was undoubtedly the most successful season of the Dandenong Thunder who managed to win the highest honors out of all tournament competition it was enrolled in. In what is now known as "The year of the Treble", Dandenong Thunder SC were crowned champions of the then State knockout Cup (re-branded Westefeild FFA Cup) while also finishing the ladder leaders on top of the Victorian Premier League (re-branded PS4 NPL) and confining their dominance in an electric VPL Grand Final finish against its season long rival Oakleigh Canons. It was the first time a VPL Final was hosted at Victoria's state of the art football stadium AAMMI Park. Marketed as a "post- A-Leauge game fixture" the VPL Grand Final gifted the Thousands of spectators a rare glimpse at just how good the quality of state football had become. In a battle beyond expectation the games events unfolded like a script even a Hollywood writer couldn't come up with. The edge of your seat, come from behind victory for Dandenong Thunder SC was a marvel of entertainment for the fans and wrote chapters in the history books of football.