FK Pelister, was formed in 1945. In 1946 they won the Bitola regional title and that same year they merged with Rabotnik. They won the Bitola title in 1950 and 1951 again. During that time the most influential players were: Georgievski, Dimitrovski, T.Petrovski, Naumovski, Lazarevski, Sekerdžievski, Avramovski, Nestorov and Eftimovski.
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.
Following the formation of the First Macedonian Football League, Pelister had early success consistently finishing in the Top 5. They also made it to the Macedonian Cup final the first two seasons coming up short both times. The club became rivals with Vardar Skopje which created the Eternal derby of Macedonia and continued the Pelagonia regional derby with Pobeda Prilep. In 2000, Pelister became the first team in independent Macedonia to reach the third phase of a European competition. They made it to round three of the 2000 UEFA Intertoto Cup, losing 1-5 on aggregate to one of the winners Celta de Vigo. Finally, the club earned its first major trophy in 2001 by winning the 2000-01 Macedonian Cup, after which they played in the UEFA Cup. In 2003, the team fell on hard times caused by financial problems and was relegated. A few years later, former players Mitko Stojkovski and Toni Micevski were able to save the club from collapse. After taking over the club they brought instant success with the team winning the 2005-06 Macedonian Second League title. The following year they made a successful comeback to the Macedonian First League and got to the 2006-07 Macedonian Cup semifinal. In the 2007-08 season, the club had its best season to date finishing in 3rd place. Once again, they played in the UEFA Cup where they lost 0-1 on aggregate to APOEL. Another case of financial difficulties and poor results, once again relegated them back to second division for the 2011-12 season. This time, however, relying mostly on young players from Bitola and led by captain Dragan Dimitrovski, Pelister made an immediate return to the top division.
The club focuses heavily on youth players from the Bitola region with a strong talent development. Gjorgji Hristov, Dragan Kanatlarovski, Toni Micevski, Nikolče Noveski, Toni Savevski and Mitko Stojkovski are some of the famous Bitola natives to start their careers with the club. Therefore, Pelister is known as the nursery of young and talented players who have left and gone to have success on various clubs in Macedonia and abroad.
The club colours have traditionally been green and white. The crest is formed in a shape of a shield, at the top left corner it has always had the number 1945 inscribed, which is the year of the club's foundation. In the latest version it includes the Cyrillic letters FK, on the right side. Shape of a mountain forms in the backdrop (to honor the mountain peak Pelister) with the name of the club in the center and a classic leather football underneath it. Early versions of the crest included the colour black, but now the entire badge uses only two colours, green and white.
Čkembari (Macedonian: Чкембари) are an Ultras group, established in 1985, who support the Macedonian sports clubs from Bitola that compete under the Pelister banner, mainly FK Pelister in football and RK Pelister in handball. The group was originally founded in 1985 when a caravan of 15 buses traveled to support RK Pelister who was playing against Partizan Bjelovar in a handball relegation play-off match. At that time they used the name BMČM - Bitolčani, Motorcyclists, Čkembari, Macedonians (Macedonian: БМЧМ - Битолчани, Мотокари, Чкембари, Македонци) later shortened to just Čkembari. Soon after, the first green and white banners were created that read: „Hell Boys“ (Macedonian: Пеколни момци) and „Green Conquerors“ (Macedonian: Зелени освојувачи) which started organized support for Pelister at every match.