[5] 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.

Present-day 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.

[6] The organization then became the chief governing body of football in the Kingdom of Yugoslavia and launched the Yugoslav First League, the first country-wide national competition held initially in a cup format.

However, the Croatian Football Federation continued to run a competition called the Croatian national football league in the territory of Independent State of Croatia (NDH), a fascist puppet state which enjoyed relative peace during World War II, and which included most of present-day countries of Croatia and Bosnia and Herzegovina.

Among others, Zagreb-based powerhouses Concordia, HAŠK and Građanski all ceased to exist, their property was nationalised, and several other clubs, most notably Dinamo Zagreb, were formed to take their place.

In the following decades Dinamo Zagreb and Hajduk Split became two of the Yugoslav Big Four (along with Belgrade-based Partizan and Red Star), a quartet of clubs which significantly dominated football in communist Yugoslavia.

On 3 June 1990 the pre-scheduled Yugoslavia–Netherlands friendly was held at the same stadium, and some 20,000 Croatian fans booed the Yugoslav national anthem and cheered for the Dutch team instead.

On 17 October 1990 the first match of the newly established Croatia national football team was held, a friendly against the United States, and following the end of the 1990–91 season Croatian clubs decided to abandon Yugoslav competitions.

After Croatia had officially declared independence on 8 October 1991, the Croatian Football Federation sought international recognition, and was finally re-admitted to FIFA on 3 July 1992 and to UEFA on 17 June 1993.