26 nations in total entered the qualifying stage. FIFA rejected the entries of Mauritius and Mozambique due to their outstanding debts, leaving 24 nations to contest the qualifying spots. Lesotho, Rwanda and Togo withdrew after the draw for the first round, which took place on 12 December 1987, but before playing a match. Libya won their first round tie and advanced to the second round, but withdrew halfway through that stage, meaning all their results in the group were annulled.
First Round: Algeria, Cameroon, Côte d'Ivoire, Egypt, Kenya, Morocco, Nigeria and Zaire, the eight best ranked teams according to FIFA, received byes and advanced to the Second Round directly. The remaining sixteen teams were paired up to play knockout matches on a home-and-away basis. The winners would advance to the Second Round.
Second Round: The eight winners from the first round were joined by the eight seeded teams and divided into four groups of four teams each. The teams would play against each other on a home-and-away basis. The group winners would advance to the Final Round.
Final Round: The four remaining teams were paired up to play knockout matches on a home-and-away basis. The winners would qualify.
Eight knockout (two-legged) ties were originally required, involving the sixteen lowest ranked African countries. The withdrawals of three teams meant only five ties were actually contested. The eight successful teams advanced to the group format of the second round.
The eight qualifiers from the first round were joined by the eight highest-ranked CAF teams. The teams were split into four groups of four which played a home-and-away round-robin, with the four group winners advancing to the final round.