The reason for formation of this church was to eliminate Serbian culture from Nazi Croatia.
The church lasted from 1942 to 1945, and was intended as a national church to which Serbs living in Croatia would convert, thus making it possible to describe them as "Croats of Orthodox faith". It had little or no popular support. It was only recognized by one other Orthodox church, the Romanian Orthodox Church, on August 4, 1944 (at the time, Romania was also under the control of the Fascist regime of Ion Antonescu). Its manager was Savić Marković Štedimlija.
The church was formed by a government statute (No. XC-800-Z-1942) on April 4, 1942. On June 5, using the statute issued by the government, the church's constitution was passed. On June 7 Germogen became the only Orthodox Metropolitan of Zagreb. The church lasted until the NDH collapsed. Germogen was shot to death the same day by partisans.
Before the Croatian Orthodox Church was formed, the NDH officially described the Eastern Orthodox Church as the "Greek-Eastern Church", and would refer to it as the "Schismatic Church" or the "Greek non-Uniate Church".
On 6 March 1993, Juraj Kolaric, dean of the Catholic Faculty of Theology in Zagreb, was reported by the Tanjug news agency as stating that the "Orthodox Church in Croatia should be organized along the Macedonian principle, with its patriarch, and break away as far as territory was concerned, from Serbia”. Kolaric had several times tried to start an initiative to start such a church and that it should be started by the "Croat Orthodox believers and possible Croatian Orthodox clergy, because then all the conditions for an autocephalous church would be met." He claimed that if a church was formed it would eventually by recognized by the Patriarch of Constantinople because the Serbian Orthodox Church would never be present in Croatia again. Kolaric claimed that his statements were not influenced by the Roman Catholic Church. The initiatives of Kolaric for the creation of such a church was protested by the Serbian Orthodox Church several times.