It is said that this Sengen Jinja was founded in 808 during the reign of the 51st emperor, Heizei, when the deity enshrined at the Fujisan Hongū Sengen Taisha was transferred via the bunrei process.  
In 1180, Minamoto Yoritomo sent an emissary,  To Taneyori, to the shrine to make an offering and pray for continuing success in war 
Taneyori was the sixth son of Chiba Tsunetane, and his visit to the shrine strengthened the already deep ties to it that his father had forged. 

When the shrine was rebuilt in 1187 three approach roads were laid out to resemble the three tracks leading upwards on Mount Fuji and the main hall was positioned to face Mt. Fuji across Tokyo Bay.

During the Edo Period the shrine grounds had an area of just over 72,700 sq.m., but following the Meiji Restoration much of the land was expropriated and the area shrank to just over 21,100 sq.m. 
The shrine was destroyed by fire in 1964 and rebuilt in 1966.

To commemorate the 60th anniversary of Emperor Hirohito’s coronation in 1986 the courtyard in front of the main hall was expanded and retaining walls built. In October 2015 a new torii was erected to commemorate the 50th anniversary of the shrine’s reconstruction.