The first ball was brought to Jagodina by the founder and director of the local male teachers school Sreten Adžić, who brought it from Vienna in 1906. However, after the end of the First World War, more precisely in 1919, the first football club was founded, after initiative of Milan Trifunović and several former Serbian soldiers, and the new club was named FK Zora. The first match was organized by Josip Baner, who had the idea when he returned home from Skopje, and the club played against a combined team of SK Jugoslavija and BSK Belgrade. FK Zora won the match by 6-0 in front of 200 spectators. In 1921, FK Zora was disbanded and a new club, named SK Sparta, was formed, but in the same year the club was banned and changed its name in JSK Budućnost, which played in the league system of the Kingdom of Yugoslavia (named Kingdom of Serbs, Croats and Slovenes until 1929). In 1923, the club won the Šumadija League, which corresponded to the third national tier. In the meantime, several teams were formed, but were later dissolved and their players formed in 1935 the football club JSK (Jagodinski sportski klub, Jagodina Sports Club). During the World War II, despite all difficulties, the JSK accomplishes major results. So in 1943, where JSK played 45 matches of which were won 32, and achieved the top position of the regional league of Morava Banovina. In the qualifications for the Serbian League, JSK defeat Šumadija Kragujevac, however, the following season was postponed and never played. Its last match in this period was played on 25 May 1944, when they won SK Karađorđe from Paraćin by 1-0.
On 5 May 1945, the day of the German capitulation, which marked the end of the war, a new club, named SD Polet, was founded and competed in the Morava League. In 1946, the club was renamed to FK Nikčević and in 1947, it reached the 1/16 finals of the Yugoslav Cup. In 1949, the club renamed again its name, this time to FK Sloga, and competed in the Kragujevac League. In 1951, the club was renamed in FK Mladost, and in 1954 to FK Morava (In 1957, FK Morava qualified for Yugoslav Second League). During this same period, other football clubs were formed in Jagodina (city of Jagodina was renamed to Svetozarevo), including the FK Mladi radnik (in 1948). In 1952, the club renamed to FK Jedinstvo. In thr same year, FK Svetozarevo was established and soon the club was renamed to OFK Kablovi, after the local cable factory. All these three clubs, FK Morava, FK Jedinstvo and OFK Kablovi are merged on 14 October, in 1962, into one single club, FK Jagodina. Despite the long history of many name changes and club mergers, the root of the club is the year of 1919, where was established FK Zora. However, FK Jagodina not recorded significant results in the following decades, and the club was located mainly in the fourth, and occasionally in the third stage of the Yugoslav football competition.
The club achieved its major success in 1993, when they promoted to the Second League of FR Yugoslavia. After a few setbacks, the club reached its new low point between 2002 and 2006, when they competed in the fourth national level. However, 2006 marked a turning point for FK Jagodina, which achieved three successive promotions, and returned in 2008 to the top flight, the Serbian SuperLiga, where it remained until nowadays. The 2011–12 Serbian SuperLiga marked FK Jagodina’s best season ever, by finishing the season on the fourth place, and thus booking a place in the 2012–13 UEFA Europa League first qualification round. The year 2012 was so far the most successful year in club's history. In addition to the reaching of the UEFA Europa League qualification round, the Jagodina City Stadium received new floodlights in November. The club finished fourth at the end of the 2012–13 season and won the 2012–13 Serbian Cup for the first time in its history.
The home field of FK Jagodina is the Jagodina City Stadium, which can hold 15,000 spectators. It dates from 1958, but was partly reconstructed in 2007. New seats were installed and the roof was constructed in the west stand along with VIP rooms. In 2009, new roof was constructed on the north stand. In November 2012, FK Jagodina installed floodlights with strength of 1,500 lux. The stadium has also a professional gym and cafe.
Further development of the stadium will include new athletic trace and reconstruction of east and south stand.