See main article: 2006 FIFA World Cup qualification (CAF). In the first round, 42 teams were paired 2-by-2 and played knockout matches home-and-away. The 21 winners would advance to the second round where they would meet the other 9 teams that qualify directly to the second round. Those teams are the 5 teams that qualified for the 2002 World Cup Finals (Cameroon, Nigeria, Senegal, South Africa and Tunisia) and the 4 highest-ranking teams in FIFA world rankings of 25 June 2003 (Congo DR, Ivory Coast, Egypt and Morocco).
| width=40% colspan=1 | Pot 1 | width=40% colspan=1 | Pot 2 |
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Mali won 4–1 on aggregate and advanced to the second round.----
Benin won 4–3 on aggregate and advanced to the second round.----
Zambia won 5–1 on aggregate and advanced to the second round.----
Botswana won 4–1 on aggregate and advanced to the second round.----
Togo won 2–1 on aggregate and advanced to the second round.----
Libya won 9–0 on aggregate and advanced to the second round.----
Kenya won 3–0 on aggregate and advanced to the second round.----
Algeria won 7–0 on aggregate and advanced to the second round.----
Uganda won 4–3 on aggregate and advanced to the second round.----
Sudan won 3–0 on aggregate and advanced to the second round.----
Zimbabwe won 4–2 on aggregate and advanced to the second round.----
Cape Verde won 4–1 on aggregate and advanced to the second round.----
Gabon won 4–1 on aggregate and advanced to the second round.----
3–3 on aggregate; Angola won on the away goals rule and advanced to the second round.----
Congo won 2–1 on aggregate and advanced to the second round.----
Malawi won 3–1 on aggregate and advanced to the second round.----
Rwanda won 4–1 on aggregate and advanced to the second round.----
Guinea won 5–3 on aggregate and advanced to the second round.----
Liberia won 3–2 on aggregate and advanced to the second round.----
Ghana won 7–0 on aggregate and advanced to the second round.----Central African Republic withdrew. Burkina Faso advanced to the second round.