Hotke-ji was built by Empress Komyo in 745, originally as a nunnery temple on the grounds where previously her father Fujiwara-no Fuhito's mansion stood. According to records kept by the temple, the initial construction went on until around 782. The temple once had a large complex with several halls and gates, and two pagodas.
Hotke-ji was heavily damaged in the fierce Siege of Nara, in 1180. In spite of reconstructions in the 12th and 13th centuries, the complex was again affected by civil conflicts during the Sengoku-era.
The current main hall, bell tower and the south gate are reconstructions of the 16th century, sponsored by Toyotomi Hideyori and his mother, Lady Yodo.
The temple's main worship statue is the wooden eleven-faced Kannon, a National Treasure. The temple also houses an ancient bath building, originally built by Empress Komyo, which she opened to the public.