The current site of Fujinomori-jinja Shrine was originally that of Mahataki-jinja Shrine (present-day Jonan-gu Shrine) and at that time Mahataki-jinja Shrine was relocated to the site on which it currently stands.
なお、現在地は元は真幡寸神社（現城南宮）の社地であり、この際に真幡寸神社も現在地に遷座した。