Of Igbo origin, Eni Njoku was born on November 6, 1917 in Ebem, Ohafia, Abia State. He was educated at Ebem Primary School and attended the Hope Waddell Training Institute, Calabar from 1933 to 1936. He attended the Yaba Higher School (now Yaba College of Technology) Lagos from 1937 to 1939.
Eni Njoku studied botany at the University of Manchester in England. He graduated with a first class honors degree in 1947 and obtained his M.A. degree the following year. In 1954, he obtained his doctorate from the University of London.
When he returned to Nigeria, Eni Njoku took up a teaching appointment at the University of Ibadan as a lecturer. Later he became a senior lecturer and then professor. He was head of the department of botany and dean of the faculty of science. He was chairman of the Electricity Corporation of Nigeria in 1956. In 1962, he became the first vice-chancellor of the University of Lagos. Following a major crisis in 1965 over his re-appointment, he resigned and became a visiting professor at Michigan State University, United States. In 1966, Njoku was appointed vice-chancellor of the University of Nigeria, Nsukka where he remained until the outbreak of the civil war in 1967.
Njoku served on the boards of the Commonwealth Scientific Committee, the United Nations Advisory Committee on the Application of Science and Technology as well as the UNESCO Advisory Committee in Natural Sciences. He also served on the councils of the Universities of Zambia and Zaire (Democratic Republic of Congo). He wrote several books and articles in international journals. He received the honorary D.Sc. degree from the University of Nigeria in 1964, and in 1966 Michigan State University conferred on him an honorary doctor of laws degree and in 1973 Unilag awarded its first vice-chancellor an honorary D.Sc. degree.
- Diamond, Larry Jay (1988). Class, Ethnicity, and Democracy in Nigeria: The Failure of the First Republic. Syracuse University Press. p. 249. ISBN 9780815624226. Retrieved 22 January 2013.
- Levi Akalazu Nwachuku; G. N. Uzoigwe (2004). Troubled Journey: Nigeria Since the Civil War (Reference, Information and Interdisciplinary Subjects Series). University press of America. p. 27. ISBN 978-0-761-8271-22.