The club was founded in 1945 and was named after Jovan Mikić Spartak, the leader of the Partisans in Subotica, who was a national hero and was killed in 1944.

When Second World War started in 1941 in Yugoslavia, Subotica was invaded by the Axis forces and incorporated into Hungary with its clubs being included in the Hungarian league system.

Some clubs such as SAND were dissolved, others like Bačka kept existing although played a much lesser role from then on, and, some new ones were formed, like Radnički or Građanski.

ŽAK Subotica kept being active for a while, however, their main sponsor, the Yugoslav Railways, decided to dissolve it and form a new club in its place which would be named "Spartak" which was the nickname of a legendary athlete from Subotica and World War II Yugoslav Partisans commander Jovan Mikić – Spartak.

Playing under the name FK Spartak Zlatibor Voda, the club started recovering finally reaching its come-back to top tier when they were promoted to the 2009–10 Serbian SuperLiga.

Spartak's biggest success since Serbia restored its name as country in 2006, came in the 2018–19 UEFA Europa League qualifying rounds.

in Round 1, then went on to achieve what is considered their brightest moment in club history defeating Czech powerhouse AC Sparta Prague over two legs.

They were eventually eliminated from the UEFA Europa League in the 3rd qualifying round, losing to Danish club Brøndby IF over two games.

After World War II, in 1951, a replacement tournament named Zentropa Cup was held to resume the rich tradition of this competition.