The organisation traces its roots to the Croatian Sports Federation (Hrvatski športski savez), which was founded on 8 October 1909 in Zagreb, at the time when Croatia was part of Austria-Hungary. The modern HNS considers its foundation date to be 13 June 1912, when the football section of the Croatian Sports Federation was established, with Milovan Zoričić as its first president.^[5] The federation reemerged on 6 August 1939 when the Banovina of Croatia was created as an administrative region within Kingdom of Yugoslavia.^[5] In April 1941 Yugoslavia was invaded by Axis Powers and was effectively dissolved. The Croatian Football Federation continued to run a competition called the Croatian national football league in the territory of Independent State of Croatia (NDH), which included most of present-day countries of Croatia and Bosnia and Herzegovina. This federation was admitted into FIFA in on 17 July 1941 HNS as the top level federation of the NDH.^[1] They fielded a team representing the NDH internationally and played fourteen international matches in the period from 1941 to 1944.^[1] Following the end of World War II, the NDH was dissolved and Croatia became a part of SFR Yugoslavia and the Belgrade-based Football Association of Yugoslavia took over as the main football-governing body in the country.^[6]

When the breakup of Yugoslavia began to unfold in the early 1990s, the political situation was reflected on football pitches. On 13 May 1990 an infamous riot occurred at Maksimir in Zagreb and interrupted the Dinamo Zagreb – Red Star league fixture. On 17 October 1990 the first match of the newly established Croatia national football team was held, a friendly against the United States. After Croatia had officially declared independence on 8 October 1991, the modern Croatian Football Federation sought international recognition and was finally admitted to FIFA on 3 July 1992 and to UEFA on 17 June 1993.^[3][1]

In February 1992 the inaugural season of the Croatian top league Prva HNL kicked off, and in March 1992 the first edition of the Croatian Cup was launched. In late 2010, the Federation held an election for its President, with Vlatko Marković opposed by Igor Štimac. Marković won by a single vote, and the assembly was marred with controversies.^[7] Štimac later appealed, calling for another meeting of the Federation.^[8] His supporters organized a new assembly and elected him the new President despite the opposing faction's boycott, leading to an impasse.^[9]

In July 2012, the federation unanimously elected Davor Šuker as president who served in the position until 2021.^[10] At the 2026 FIFA World Cup, the federation filed a formal complaint against FIFA over improper use of snickometer-enabled VAR during Croatia's 2–1 defeat to Portugal.^[11] They argued that the equalizing 103rd-minute stoppage-time goal from Joško Gvardiol was incorrectly disallowed as offside according to the rules of the game.^[12]