In 1950 Lipkin emigrated to Israel with his wife Malka, partly to become involved with the Kibbutz movement. Instead of agricultural work, the Israeli government assigned him to spend a year at CEA Saclay, a French Atomic Energy Commission facility, to acquire knowledge to support the planned opening of Israel's first nuclear reactor at Dimona. In 1954 he returned to work in Israel, establishing the country's first course in nuclear physics at the Weizmann Institute of Science in Rehovot. Between 1956 and 1958 he served as an advisor to the United Nations Atomic Energy Commission. In later years he worked frequently with the Argonne National Laboratory in the United States. In 2007 Lipkin was working at the Weizmann Institute and at the Sackler Institute of Tel Aviv University.