The club was formed in 1932 under the name RSD Šibenik. The first president, Dr Martin Čičin-Šain, was only appointed to this role during the first board meeting which was held in August 1933. They played in a stadium in the area of Crnica, next to the La Dalmatienne factory in Koprivnica. The playing field was officially opened on 31 May 1936. The first matches played were part of a 1936 tournament between Šibenik, Osvit, Split and AŠK. Around the same time the first registered football club in Šibenik was also formed. This club was called Osvit and it was responsible for the construction of Stadion Šubićevac.
The club played its first official league match in 1946 under the name FD Šibenik and the very next year it was crowned the champion of the Dalmatia region. The club's new home ground was opened on 1 May 1948 and bore the name of "the people's hero" Rade Končar. In 1950–51, Šibenik finished top of the Croatian Republic League and gained promotion to the Yugoslav Second League for the first time in their history. However, they were relegated immediately and it was not until 1954–55 that they returned to the second division. In 1957, the club made it to the semi-final of the Yugoslav Cup.
In the 2011–12 Prva HNL season, the club finished 14th and were relegated to Druga HNL. In the following season, Šibenik finished 4th, but due to financial difficulties, they were once again relegated to Treća HNL. In the 2013-14 season, Šibenik finished in second place with their marksman Miro Slavica scoring 30 goals to take out the league's top goalscorer award, but failed to lead his side to promotion.
At the end of the 2014–15 season, Šibenik gained promotion to Druga HNL, topping the 3. HNL - Jug. Mirko Labrović took over as manager in 2015.