Michael Ugwuja Eneja was born to pagan parents Eneja Nwa-Ugwuokeja and his wife Maria Mboka Ajibo Nwamkpozi during 'the planting season of the year after the influenza which ended in 1918.' Bishop Eneja rightly put the date to 1919. He is a native of Ibagwa-ani in Nsukka area of Enugu State, Nigeria.

Born at a time when the new Western civilisation brought about by the British colonial government was slowly creeping into Igboland, Michael willingly embraced the new ways, which involved attending school to receive western education and attending church to become a Christian. This choice was not without troubles and difficulties. In the first place, boys of his age, at that time, had to run into the bushes and farmlands to evade recruitment into the Whiteman's school, and Michael was viewed as a fool by sundry people in the village for not doing the same. Furthermore, Michael came from a traditional priestly family of a very popular and powerful deity called Abodo Owerre. His immediate father was, at that time, the chief priest of this deity, and Michael (Ugwuja) was a possible candidate who, by divination, could succeed him.

So, disappointed and angered by what was perceived as treachery, his parents ostracised him and sent him away from the family house. Thus, at a very tender age, Michael had already begun to manifest heroic faith, enduring persecutions from his loved ones and refusing to conform to a tradition he disdained. He was unwavering in the face of ostracism. He took temporary refuge in the home of Maria Asogwa, a Christian convert who had left her family compound to settle in another house to avoid contact with her pagan husband, Asogwa Nwugwu Ogbene. Here, Michael met and became intimate friends with Maria's son Simon, who was four or five years older than him. It was Simon who taught him prayers while the duo attended school and church together. However, he was later recalled to the family by his parents, who were not ready to lose him completely.

He started elementary school in 1928 at the age of 9 at the mission church school situated near Nwayo market in Ejuonu Ibagwa-ani. His first teacher was Mr. Louis Orakwe from Umoji, Idemili Local Government Area of Anambra State, Nigeria. He became Orakwe's house boy and followed him on his transfer to Nsukka, where Orakwe doubled as teacher and catechist. It was at Nsukka, still under the tutelage of Mr. Orakwe, that Michael was baptised in 1930 by Fr. Davey, the then parish priest of Eke from where Nsukka was administered. Five other boys baptised along with him were James Ugwuja, Dominic Ugwuoke, Felix Ugwuja, John Onyishi, and John Ukwueze. Louis Orakwe was his master, teacher and baptismal sponsor.

In 1931, Michael left Ibagwa-ani and became a pupil at Umundu/Igugu school in Udenu L.G.A. under a new master, Mr. Ignatius Okwu from Mgbugbu-owa in Ezeagu L.G.A. Here, he did Standards One and Two between 1931 and 1932, and in 1933, he was sent to St. Paul's Eke to continue from Standard Three. However, Eke down-graded him to Standard Two for the reason that he came from a 'bush school' and was not exposed to some courses taught at Eke. Life became tough at Eke with regard to feeding as borders were required to cook for themselves. They had to go home every weekend to replenish their food stock for the following week.

It was not an easy task to trek to and from Eke to Ibagwa-Ani every week. Again, divine providence came to his rescue. His master, Mr. Okwu, whose Mgbagbu-Owa village was much closer to Eke than Ibagwa-Ani, arranged for him to collect foodstuffs from his people. When Mr. Ukwu left the teaching service and took employment with the Nigerian Railways, Michael became a house boy to yet another Master, Mr. Edmund Udenta, a native of Ogwofia Owa in Awgu Local Government. He lived with him and received free food till he finished his Standard Six.

The Eke primary school was located in the same place as St. Paul's Major Seminary, which eventually became Bigard Memorial Seminary, Enugu, after a series of other movements. Michael's inspiration for priestly life came from his contact with Michael Tansi (now Blessed Tansi) from Aguleri. Michael was then in Standard Two at Eke. As Bishop, Michael Eneja recalled that association with seminarians at Eke – including Michael Tansi, Joseph Nwanegbo, William Obelagu – who were doing a four-year theological course at the Eke seminary must have helped me a lot.' The seminarians taught the primary school pupils church music, how to serve at Mass, and preached to the boarders. He also recalled his Standard Six teacher, William Onuchukwu, who was always talking about priestly vocation.

After Standard Six at Eke 1937, Michael was employed as a Teacher in Eke Parish in 1938, and within one year, he was able to teach as needs arose in three stations—Umulumgbe, Okpatu and Egede. In 1939, he entered the Junior Seminary, which was then in Christ the King College Onitsha and successfully did his Senior Cambridge Certificate Examination in 1942. Thus began his journey to the priesthood.