Lee was born in 1924 in Butterworth, Penang, and was educated at Yeok Keow Chinese School and Chung Ling High School in George Town, Penang.
During the Japanese occupation of Penang, he took refuge in his uncle's farm located in a jungle.
From 1959 to 195? he studied journalism at Regent Street Polytechnic in London.
In 1946 Lee commenced a career in journalism in Penang with Sin Pin Jit Poh, then left for Singapore to work for a number of Chinese (Sin Chew Jit Poh, Nanyang Siang Pau) and English (Singapore Standard) newspapers before culminating in his working for The Straits Times in 1957.
Resigning in 1959, Lee commenced his political career and was elected to the legislative assembly. He served as Minister of State for Culture, Minister of State in the Prime Minister's Office (PMO), Senior Minister of State for Foreign Affairs, and Senior Minister of State in PMO. He stepped down from his parliamentary positions in 1984.
In 1968 he commenced his diplomatic career, serving as Singapore's Ambassador to Egypt, Ethiopia, Yugoslavia, Lebanon and Indonesia, and High Commissioner in Pakistan. On stepping down from Parliament, he served as Singapore's Ambassador to Japan and South Korea.
He retired from public service in 1988, founding his own firm, Eng Lee Investment Consultants, in 1990.
He has been and is a director of a number of companies. He is currently Chairman of Eng Lee Investment Consultants, and an Independent non-executive director of Koh Brothers Group Ltd. Previous positions held include:Chairman, Sino-American (UIC) Tours Corporation
independent director, Metro Holdings
Non-Executive chairman, SSH Corporation (formerly known as Sin Soon Huat)
independent director, L & M Group Investments
Since 1966 Lee has published ten books, including:Lee, Khoon Choy (2013) Golden Dragon and Purple Phoenix: The Chinese and Their Multi-Ethnic Descendants in Southeast Asia. Hackensack, New Jersey: World Scientific. 2013. p. 604. ISBN 978-981-4383-43-1.
Lee, Khoon Choy (2005) Pioneers of Modern China: Understanding the Inscrutable Chinese. Hackensack, New Jersey: World Scientific. 2005. p. 576. ISBN 978-981-256-618-8.
Lee, Khoon Choy (1999) A fragile nation: the Indonesian crisis. World Scientific Publishing.
Lee, Khoon Choy (1995) Japan: Between Myth and Reality. World Scientific Publishing. ISBN 9810218656, 9789810218652.
Lee, Khoon Choy (1993) Diplomacy of a Tiny State. World Scientific Publishing. ISBN 9810212194.
Lee, Khoon Choy (1976) Indonesia: Between Myth and Reality.
Lee's hobbies included painting and playing musical instruments. Lee married Florence Khor Swee Hoon, and they had two sons. She died of cancer at age 30 in 1959. In 1962 he married Eng Ah Siam, with whom he has had five daughters. Lee died in his sleep at home aged 92, at 3am on 27 February 2016. He is survived by his second wife, seven children and 11 grandchildren.
Lee was one of the last People's Action Party (PAP) old guard office holders still alive. Other PAP members of his generation include Othman Wok, Jek Yeun Thong, Chor Yeok Eng and Ong Pang Boon. Lee's death was the first to follow the death of party founder Lee Kuan Yew.1974: (Indonesian) Bintang Bakti Utama (Meritorious Service Star) for his work in enhancing relations between Indonesia and Singapore.
1986: The Scholarly Achievement Award by the Japan Institute of Oriental Philosophy for his achievements in the research and development of eastern philosophy, thought and culture.
1988: (South Korean) Order of Diplomatic Service Merit for his service in promoting relations between South Korea and Singapore.
1990: (Singaporean) Darjah Utama Bakti Cemerlang (Distinguished Service Order) in recognition of his contributions.
1997: Made an honorary member of the Chinese National Academy of Social Sciences in Beijing for his contributions in the field of humanities and social sciences.