The club was formed as RK Naissus on 7 September 2009 by the amalgamation of RK Železničar and ORK Niš. They immediately started competing in the Serbian Handball Super League by inheriting the spot from ORK Niš.
On 5 December 2011, the club changed its name to RK Železničar. They won their first trophy, the Serbian Handball Cup, in the 2013–14 season. After suffering relegation from the top flight in 2016, the club spent the following season without competing.
Ahead of the 2017–18 season, the club received a wild card entry to the Serbian Handball Super League.