Mustapha El-Kanemi was born in 1924, fourth son of the 17th Shehu of Borno, Sir Umar ibn Mohammed El-Kanemi, and was brought up in Dikwa, Borno State.
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He attended Government College Maiduguri for his secondary education, and in 1975 was admitted to the Staff Training Centre, Potiskum where he obtained the Intermediate Local Government Certificate.