The team played primarily in the lower divisions of the former SFR Yugoslavia and were champions of the Macedonian Republic League four times, along with winning the Macedonian Republic Cup four times in 1959, 1962, 1985 and 1991. They earned promotion to the Yugoslav Second League Group East, which included clubs from Serbia, Montenegro and Macedonia, for the first time in 1974, which was a big success for that generation. Some of the most famous players at the time were: Grbevski, Dukovski, Cvetkovski, Taškov, Bogoevski, Gočevski, Ristevski, Tristovski, Mickovski, Dimovski, Markovski, Upalevski and the manager Stavre Eftimovski. Soon after, they were relegated but made another comeback in 1982 with Mitko Butlevski as chairman and Ivan Čabrinović as manager. The biggest success came in the 1990–91 Yugoslav Cup when they reached the 1/8 final, getting eliminated on away goals by the eventual champions Hajduk Split. Pelister played their final season in the Yugoslav league system in the 1991–92 Yugoslav First League finishing in 15th place.