In 1228 during the Kamakura period, the Kamo-gawa River flooded due to heavy rain, but the rain stopped and the floodwater subsided when the Nakahara (中原) clan who served as Bokashi (administration of the Kamo-gawa River) prayed to the Jizo statue for the rain to stop, and the temple was granted the name 'Chugen-ji Temple' (仲源寺, which are expressed in 'naka' (中) and 'hara' (原) added right-hand radical of each Chinese character, meaning 'human' (人) and 'water' (水) respectively) by the imperial court.
鎌倉時代の1228年（安貞2年）鴨川が大雨で洪水となり、防鴨河使となった中原氏がこの地蔵尊に止雨を祈ったところ雨がやんで洪水も治まったことから、朝廷から「仲源寺」の寺号を下賜されたという。