Basque-born Fr. Arrupe joined the Society of Jesus in 1927. Because of the order of expulsion by the Republican government of Spain at the time, all Jesuits were sent into exile. Accordingly he pursued his philosophical and theological studies in Belgium and the Netherlands. Ordained a priest in 1936 and sent off for doctoral studies in medical ethics in the United States, he was unexpectedly sent as a missionary to Japan in 1939.
He was appointed Jesuit superior and the master of novices in Japan in 1942. He was living in suburban Hiroshima when the atomic bomb fell in August of 1945. He described that event as "a permanent experience outside of history, engraved on my memory." He utilized his medical skills in the service of the wounded and the dying, transforming the novitiate into a make-shift hospital for over 200 greviously scarred human remnants. He eventually was appointed the provincial superior of the Jesuits in the Japanese province.
At the 31st General Congregation of the Society of Jesus in 1965 he was elected to be the order's 28th Superior General. He served in that position from 1965 to 1981.