This shrine was important as the general guardian shrine for Shinjuku from even before the start of the Edo Shogunate under Tokugawa Ieyasu (1603). It is thought that the shrine was established by bringing a deity from the Yoshino mountains in the Yamato Province before 1590, when Tokugawa Ieyasu received the Musashi province. The shrine was called Inari from the Edo period, but as the name Inari is most often used to refer to the Fushimi Inari Shrine, on January 25th 1916, a Shinto priest named Torii, a representative of shrine parishioners named Sakata, and thirteen others petitioned the governor of Tokyo prefecture to change the name of the shrine. Permission to change the name was granted on February 26th 1916, and the shrine became the Hanazono Inari Shrine. In 1965, the shrine finally became known as the Hanazono Shinto Shrine when the deity from the subordinate Ootori Shrine was enshrined there at the time of the rebuilding of the Ootori Shrine.