In its long and rich history, FC Pelister was formed way back in 1924, first under the name Omladina, then Pelister and afterwards SC Bitola, putting together some of the most talented players at that time: Kogo Džima, Kacujani, Temelkovski, Hroni and Čomo. In 1945, the club was renamed back to Pelister and won the Bitola regional title in 1946. That same year, it fused with Rabotnik, but it kept the name Pelister.

Team played primarily in lower divisions of the former Yugoslavia and was champion of the Macedonian Republic League for four times, along with winning the Macedonian Republic Cup in 1990. They earned promotion to the Yugoslav Second League for the first time in 1974, which was a big success for that generation. Soon after, they were relegated but made another comeback in 1982. The biggest success came in 1990/91 Yugoslav Cup, when they reached the 1/8 final, getting eliminated on away goals by the future champion Hajduk Split. Before the fall of the former Yugoslavia, Pelister played in the final season of the Yugoslav First League finishing in the 15th place.

Since the formation of the Macedonian First 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. In 2000, Pelister became the first team in independent Macedonia to reach the third phase of the European competition. They made it to the round three of 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 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 saved the club from collapse. After taking over the club, they brought instant success with the team winning 2005/06 Macedonian Second League title. Following year, they made a successful comeback to the Macedonian First League and got to 2006/07 Macedonian Cup semifinal. In 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 during 2011/12 season. This time, however, relying mostly on young players from Bitola and led by captain Dragan Dimitrovski, Pelister won instant promotion to the top division.

Club focuses heavily on youth players from the Bitola region with a strong talent development. 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. However, apart from developing its players’ psychical competences, Club is also focused on their personal development, nurturing the spirit of tolerance, friendship and fair-play in its multicultural framework.