The 1946 Croatian Football Championship was a two-stage competition for clubs from PR Croatia which served as a qualifying tournament for the new post-war First League in communist Yugoslavia, and its inaugural 1946–47 edition.
Through a series of regional preliminaries and playoffs eight clubs earned a spot in the final stage, in which they played each other twice in a 14-round double round-robin format.
A separate qualifying tournament was organized for clubs from the newly acquired territories of Istria and the city of Rijeka (Fiume).
The newly established SD Kvarner (also known as "SCF Quarnero" in Italian) from Rijeka won a playoff against US Operaia from Pula to represent the military-administered Zone B, in the Julian March.
Also played FD Crikvenica, Omladinac Senj, Plavi Jadran Pag, NK Naprijed Hreljin Bjelovar qualified to play-offs.