The alphamegalog of African cities lists the largest city in Africa for each letter of the alphabet. In this case, ‘largest’ is based on population within the city proper.

Alexandria, Egypt
Brazzaville, Congo
Cairo, Egypt
Dar Es Salaam, Tanzania
Ekurhuleni, South Africa
Freetown, Sierra Leone
Gaza, Egypt
Harare, Zimbabwe
Ibadan, Nigeria
Johannesburg, South Africa
Kinshasa, DR Congo
Lagos, Nigeria
Mogadishu, Somalia
Nairobi, Kenya
Omdurman, Sudan
Pretoria, South Africa
Qadarif, Sudan
Rabat, Morocco
Soweto, South Africa
Tripoli, Libya
Ubungo, Tanzania
Vihiga, Kenya
West Rand, South Africa
Xanthia, South Africa
Yaoundé, Cameroon
Zaria, Nigeria