A shrine enshrining Sanetsumu SANJO was constructed on the ruins of the Sanjo family estate by the order of Imperial Prince Kuninomiya Asahiko and it was formally founded in 1885 when it was given the name Nashinoki-jinja Shrine after the area in which it is located and the shrine rank of Bekkaku Kanpeisha.
久邇宮朝彦親王の令旨により、三條家の邸宅跡に三條實萬を祀るための社殿を造営し、明治18年（1885年）、地名からとった梨木神社の社号と別格官幣社の列格を受けて創建した。