Some documents written in the late Kamakura period had already told that the temple was called, as synonyms, Tomoe-dera Temple, Mumyoan (house of anonymity), Kiso-zuka, Kiso-dera Temple, and Gichu-ji Temple.
寺は別名、巴寺、無名庵、木曽塚、木曽寺、また義仲寺と呼ばれたという記述が、すでに鎌倉時代後期の文書にみられるという。