According to the legend passed down at the Mikubi-jinja Shrine (literally, "Shrine of the Honored Head), Masakado's was felled by an arrow loosed by the god Hayato-shin, who is enshrined at the Nangu-taisha Shrine in Mino; Masakado was enshrined and worshipped as a god at the place where he fell, and the Mikubi-jinja Shrine was built in order to appease Masakado's anger and console his spirit so that his head would not return to the eastern provinces.
御首神社に伝わる話では将門の首は、美濃の地で南宮大社に祭られていた隼人神が放った矢によって射落されてしまう、落ちた場所に将門を神として崇め祀り、その首が再び東国に戻らないようにその怒りを鎮め霊を慰めるために御首神社が建てられたという。