Returning to Singapore, Nathan received his primary education in Anglo-Chinese Primary School and Rangoon Road Afternoon School, and his secondary education at Victoria School. However, he was expelled from school twice and, after quarrelling with his mother, ran away from home at the age of 16. During the Japanese occupation of Singapore, Nathan learned Japanese and worked for the Japanese civilian police as a translator. After the war, whilst working, he completed his secondary education through a correspondence course with Wolsey Hall, Oxford, and entered the University of Malaya (then in Singapore), where he became the secretary of the University Socialist Club in his second year of university. He graduated in 1954 with a Diploma in Social Studies (Distinction). He earned a diploma from the University of Malaya in Singapore in 1954. This was followed by a long career in the Singapore Civil Service, which he joined in 1955. Between 1962 and 1966 he was seconded to the National Trades Union Congress, and then worked in the Ministry of Foreign Affairs and Ministry of Home Affairs. He was with the Security and Intelligence Division of the Defence Ministry when the Laju incident happened in 1974, and was among the government officers who agreed to accompany terrorists who had bombed petroleum tanks to Kuwait to secure the release of civilian hostages and ensure the terrorists' safe passage. He served as First Permanent Secretary of the Foreign Ministry from 1979 to 1982.