Born on November 6, 1917, in Ebem, Ohafia, Abia State, Eni Njoku was educated at Ebem Primary School and attended Hope Waddell Training Institute, Calabar between 1933 and 1936. He went to Yaba Higher School (now Yaba College of Technology) Lagos in 1937.
Njoku studied botany at the University of Manchester in England. He graduated with a first class honours 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, Njoku took up teaching appointment at the University of Ibadan as a lecturer. Later he became a senior lecturer and then professor. He was head 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 the Michigan State University, the USA in 1966; Njoku was made the 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 in 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.