In 1924 Aptowitzer was invited to an academic position in Jerusalem but he turned down the offer because of his wife's illness. In 1938, after his wife died, Aptowitzer emigrated to Palestine, but by this time there was no position available for him. In Israel he was engaged primarily in editing his papers for publication. Aptowitzer died December 5, 1942 and was buried in Jerusalem's Mount of Olives cemetery. In his last will and testament he asked that his tombstone only state that he edited the works of Ra'avyah; he also asked that his unpublished writings be burned. Throughout his life he suffered from a number of diseases and shortness of vision and in his later years he was blind.