The site of Jojakko-ji Temple is reputed to have been the location of FUJIWARA no Sadaie's villa 'Shigure-tei' during the Heian period and the temple was founded in 1596 at the end of the Azuchi Momoyama period in order to serve as a place of retirement for Nittei, 6th chief priest of the Nichiren Sect Daihonzan (Head Temple) Honkoku-ji Temple.
平安時代に藤原定家の山荘「時雨亭」があったと伝わる地で、安土桃山時代末の慶長元年（1596年）に日蓮宗大本山本圀寺十六世日禎が隠棲の地として当山を開いた。