Nathan began his career in the Singapore Civil Service as a medical social worker in 1955. He was appointed Seamen's Welfare Officer the following year. In 1962, he was seconded to the Labour Research Unit of the National Trades Union Congress (NTUC), first as Assistant Director and later as Director of the Labour Research Unit until January 1966. Nathan negotiated Singapore's membership of the Afro-Asian People's Solidarity Organisation. He later served as a member of the NTUC's Board of Trustees from 1983 to April 1988.