He died in 1646 and was buried in the Hotoku-ji Temple located in Yagyu shimo-cho, Nara City, which was founded by himself to pray for the repose of his father's soul, having invited his friend Takuan Soho as the first chief priest.
正保3年（1646年）に没し、自身が父の菩提を弔うために友人の沢庵宗彭を招いて柳生に開いた奈良市柳生下町の芳徳寺に葬られた。