In 1936, he was enrolled at Church of Scotland Mission (CSM) Primary School Gīthīga. Upon starting formal schooling, he became a follower of the CSM, which is the earlier name of the Presbyterian Church of East Africa (PCEA).
He was eight years old, two years older than the standard admission age for the first grade today. Njenga passed the Common Entrance Examination and qualified to join the intermediate level in Kikuyu, then called Thogoto Scotland Mission Intermediate School.
Unfortunately, this was not to be. The 100 Kshs annual fee was far beyond what his parents could afford. Fortunately, in 1940, he was admitted at the Catholic School in Lioki that was charging 24 Kshs yearly fee. While in Lioki, he underwent the Agĩkũyũ initiation rites and received the Sacraments of Christian initiation namely: Baptism and Confirmation. Soon, he gained an interest in deepening his faith through frequenting catechism classes.
In the midst of this, he exhibited stable signs of becoming a Priest. The dedication of Frs. Austin Lynch and Ted Colleton acted as a powerful pull towards his interest in the priesthood. In 1943, he sat for his final examinations in which it emerged that out of 20 candidates only two had attained the required points for admission into high school.
The successful students were John Njũgũna and John Njenga. The Catholic run Holy Ghost College, which later became Mang’u High School, unhesitatingly offered him a place, since as was its tradition then as it is now, the school only admitted the best candidates in the country. At Mangu, his love for God bloomed. He became a member of the Legion of Mary and taught catechism to his schoolmates.
His contemporaries at Mang’u included Dr. Lawrence Sagini, Moody Awori (whom he personally taught catechism), Prof. Mwinzi, Titus Mbathi, Tom Mboya, Michael Njenga and the retired president Emilio Mwai Kibaki. Due to his trademark priestly demeanor, his fellow students nicknamed him kamũbea (a little priest). Back in Mang’u, he excelled in Mathematics and the Physical Sciences. In 1947, he sat for the prestigious Cambridge School Certificate Examination and scored a First Division.