Born in Oshodi, Lagos State, Awojobi's father, Chief Daniel Adekoya Awojobi, was a stationmaster at the Nigerian Railway Corporation who hailed from Ikorodu in Lagos State. His mother, Comfort Bamidele Awojobi (née Adetunji), was a petty trader who hailed from Modakeke, Ile-Ife, Osun State. Between 1942 and 1947, he attended St. Peter's Primary School, Faji, Lagos.
It was while at his secondary school, the CMS Grammar School, Lagos, that his academic traits began to manifest. Not only was he seen to be gifted in mathematics and the sciences, he was comfortable also in the arts, becoming a member of the school's literary and debating society. It was during this period that he earned the nickname, "Macbeth": William Shakespeare's famous play, Macbeth, was to be staged in the school. The lead actor took ill a week before, and so Ayodele was called upon to play the lead role in his stead. It is said that not only did Ayodele master his lines as lead actor, but also the entire play, such that he was able to prompt the cast whenever they forgot their lines.
Ayodele was a straight-A's secondary school student, while at the CMS Grammar school, passing his West African School Certificate examinations with a record eight distinctions in 1955. He proceeded to the Nigerian College of Arts, Science and Technology, Ibadan, for his General Certificate of Examinations, GCE (Advanced Level), where in 1958 he sat for, and obtained distinctions in all his papers: Physics, Pure Mathematics and Applied Mathematics. In 1962 Awojobi was awarded his first degree in Mechanical Engineering – a BSc (Eng) London, with first class honours, at the then Nigerian College of Arts, Science and Technology, Zaria (now Ahmadu Bello University, Zaria).
It was said by Akintola Ajai (himself an engineering graduate of the University of London), that when Awojobi arrived at the Nigerian College of Arts, Science and Technology, Zaria, he boasted openly saying that it was his intention to finish the whole course within a period of three years only; an impracticable feat due to the fact that nowhere was the BSc Mechanical Engineering curriculum designed to run less than four years. Ayodele accomplished it in three years just as he had predicted.
The federal government awarded Awojobi another scholarship in 1962 to study further at the post-graduate level in the field of Mechanical Engineering at the Imperial College of the University of London (now Imperial College London). He completed the course, successfully defending his thesis, and was awarded a PhD in Mechanical Engineering in 1966.
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