Spartak was founded in 1945, as a successor to pre-WWII ZAK (Zeleznicarski Atletski Klub/Railways Athletes Club) founded in 1921. ZAK participated in 1936 Kingdom of Yugoslavia national championship with Spartak adapting club colours, football ground and most of pre-WWII ZAK players upon foundation taking place on 21st of April 1945.
New club was named in memory of Jovan Mikic Spartak, member of national athletics team, triple jump and penthatlon state record holder.
As soon as 1946, Spartak became member of Yugoslav top-tier and got relegated and promoted back to the elite on number of occasions. Tough times and ecomonical troubles led to Spartak being relegated to third-tier at some point but new era started in 2004 followed by successful club`s comeback and quick rise from third to top-tier in a matter of just few seasons. Spartak was promoted to Serbian Super League in 2009 and the club never looked back.
Moreover, Spartak won fourth place at the end of 2009/2010 season, to mark club`s successful comeback to the top-tier. Spartak also reached two national cup semi-finals in 2013/2014 and 2015/2016 seasons.
Until summer of 2013, Spartak competed under Spartak Zlatibor Voda name – Zlatibor Voda being club`s former sponsor – followed by club`s board decision to change the name back to FK Spartak. Club changed name once again starting from the 2016/2017 season adding new sponsor Zdrepceva Krv to club`s name.
In 2010/2011 and 2018/2019 seasons, Spartak took part in UEFA Cup/UEFA Europa League. In 2010 competiton, Spartak started from round 2 qualifiers eliminating Differdange 03 of Luxembourg 5-3 on aggregate (3-3 away, 2-0 home) but got eliminated in a next round by Dnipro of Ukraine, competitions runners-up from 2014/2015 season. Dnipro Dnipropetrovsk eliminated Spartak 3-2 on agg. Spartak won first leg 2-1 at home but lost away in Ukraine 2-0. In 2018/2019 season, Spartak won round 1 tie against Nortern Irish outfit Coleraine 3-1 on agg (1-1 home, 2-0 away) followed by round 2 elimination of Sparta Prague (2-0 home, 1-2 away) but round 3 opponent Brondby proved to tough and Spartak lost home tie played in Belgrade 2-0 followed by 2-1 defeat in Denmark. Spartak actually played all mentioned UEFA competition home games at Novi Sad`s Karadjordje Stadium (Differdange 03, Dnipro, Coleraine, Sparta) and Belgrade`s Rajko Mitic Stadium (Brondby) as club`s home ground failed to meet UEFA stadium regulations licence.