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NPL WA traces its origin to the formation of a league by the Perth British Football Association in 1896. By the 1950s, the association was known as the Western Australian Soccer Football Association (WASFA). In, 1960 eight teams formed their own association, the Soccer Federation of Western Australia (SFWA). The WASFA and SFWA ran rival leagues between 1960 and 1962 before the SFWA prevailed. Ahead of the 1991 season, 11 SFWA clubs broke away, forming the Soccer Administration of Western Australia (SAWA). The SAWA ran the rebel Professional Soccer League (PSL) in parallel with the SFWA first division until merging before the 1993 season to form the Professional Soccer Federation of Western Australia (PSF).

Several of the clubs currently playing in the league were formed as the soccer arm of cultural associations of recently migrated Australians, with certain teams having associations with particularly nationalities e.g. Swan Italian Club (now Swan United), Bayswater Inter (now Bayswater City) and Perth Italia (now Perth SC) with Italian Australians, Morley Windmills with Dutch Australians, Floreat Athena with Greek Australians, Benfica United (now Fremantle Spirit) with Portuguese Australians, Inglewood Kiev (now Inglewood United) with Ukrainian Australians, North Perth Croatia (now Western Knights) with Croatian Australians, Spearwood Dalmatinac (now part of Cockburn City) with Yugoslavian Australians, Shamrock Rovers with Irish Australians, Dianella White Eagles with Serbian Australians and Stirling Macedonia with Macedonian Australians. In 1994 clubs were forced by the sport's governing body to remove all references to ethnicities from their names, which resulted in several forced name changes. Some clubs reverted back to their former names after 2019, when the National Club Identity Policy was revoked. More recently, new clubs have begun to be based geographically, such as with Armadale SC and Cockburn City.

The West Australian National Training Centre included a team for the 2011–2013 seasons. They did not play for competition points, and were mostly used for development of the upcoming youth players.