The shrine became the object of Imperial patronage during the early Heian period. In 965, Emperor Murakami ordered that Imperial messengers were sent to report important events to the guardian kami of Japan. These heihaku were initially presented to 16 shrines; and in 991, Emperor Ichijō added three more shrines to Murakami's list. Three years later in 994, Ichijō refined the scope of that composite list by adding Umenomiya Shrine and Gion Shrine, which is now known as Yasaka Jinja.
In 1039, Emperor Go-Suzaku ordered that one more shrine be added to the grouping created by Murakami and Ichijō -- the Hie jinja. This unique number of Imperial-designated shrines has not been altered since that time.
From 1871 through 1946, the Hie jinja was officially designated one of the Kanpei-taisha(官幣大社?), meaning that it stood in the first rank of government supported shrines.