The club was formed in 1932 under the name RSD Šibenik. The first president, dr. Martin Čičin-Šain, wasn't appointed until the first board meeting which was held in August the following year. 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 the 31st of May, 1936. The first matches played there was a tournament between home side Šibenik, Osvit, Split and AŠK that same year. Around the same time the first registered football club in Šibenik was also formed. This club was called Osvit and built the stadium Šubićevac.
The club played its first official league match in 1946 under the name FD Šibenik and very next year was the champion of the Dalmatia region. The club's new home ground was opened on the 1st of May 1948 and bore the name of "the people's hero" Rade Končar. Šibenik finished top of the Republic League and so were promoted to the second division for the first time in their history in 1950/51. However, they were relegated immediately and it was not until 54/55 until they were promoted again to the second division. In 1957, the club made it to the semi finals of the Yugoslav Cup.
In the season 2011-12 HNK Sibenik won 14th place in the 1. HNL and competition rules in the season 2012/13. continues to compete in the 2nd Division. In the season 2012-13 HNK Sibenik won 4th place in the 2. HNL but due to financial problems will continue to compete in the 3rd Division. In the season 2013/14. they won 2nd place in the 3rd Division - South and fails to qualify for the higher ranking competition.