HC Vardar was founded in 1961, as part of the Vardar Sports Club in Skopje, which has been existing since 1947. The club began to rise to power in the last decade of the past century. HC Vardar is a record-breaker having become a Macedonian champion 10 times (1998/1999, 2000/2001, 2001/2002, 2002/2003, 2003/2004, 2006/2007, 2008/2009, 2012/2013, 2014/2015 анд 2015/2016) and a winner of Macedonian Cup eight times (1997, 2000, 2001, 2003, 2004, 2007, 2008, 2012, 2013, 2014 and 2015). By that HC Vardar is superior to other handball clubs in Macedonia.
HC Vardar participated for the first time in the 1993/1994 season in the EHF Cups matches in Europe. The club took part in the EHF Champions League seven times. In the 2013-2014 season HC Vardar is participating for eighth time in the most elite European competition among the clubs.
HC Vardar became a semifinalist three times in the Super Cup (1998/99, 2004/05 and 2010/11), participated one time in the quarter-final of the Super Cup (2006/07) and became a quarterfinalist one time of the Challenge Cup (2005/06). During its first European semi-final of the 1998/99 season, HC Vardar was defeated by Ademar Leon's team (27:29, 20:35). The club couldn't outplay HC Zagreb (23:21, 26:34) during the second semi-final of the Super Cup (2004/2005) and during the third attempt (2010/2011) the impassable barrier for the team was Gummersbach (21:33, 29:38).
In season 2016/17, the club achieved the biggest success, becoming European champion triumphing at the F4 tournament in Cologne. On the way to that success Barcelona were defeated in the semi-finals, and PSG in the final.
Vardar is the first winner of the Regional SEHA League. On 15 April 2012, Vardar defeated Metalurg at the Zagreb final to become the first SEHA League champion. The second season in the SEHA League Vardar finished with the title of vice-champion after HC Zagreb's defeat at F4 tournament final in Skopje.
Last season won the fourth trophy in the SEHA Gazprom League on home field in its Jane Sandanski arena becoming the only club with four cups won in competition.
After a three year break Vardar has again become a national champion winning its eighth Macedonian champion title at the end of the 2012/2013 season.
The club started a new 2013/2014 season with new management structure. Sergey Samsonenko is a new proprietary and a sport director of the club, Mihajlo Mihajlovski has become an honorary club chairman.
HC Vardar will play the National Super League and the Regional SEHA League matches of 2013/2014 season in the SC „Kale" in Skopje (2.500 places), and the EHF Champions League matches will be held in the SC „Boris Trajkovski" in Skopje (6.170 places).
Now HC Vardar play in his own arena S.C. Jane Sandanski (6.500 places).