After being given a walk-over following Kenya's withdrawal from the 1998 Championship, the team made it to the finals in Nigeria, where they lost 0–8 to the hosts before beating Egypt 4–1. Morocco met fellow Women's African Football Championship debutants Republic of Congo in the final group game, with both teams having the chance to qualify for the semi-finals with a win. However, the eventual 0–0 draw sent Morocco out, as Congo qualified on better goal difference.
Two years later, Morocco qualified for the African Championship in South Africa with a 6–1 aggregate victory over Algeria. However, after the team scored the first goal against Cameroon in the opening group stage match, they went on to concede 13 goals, lose all three matches, and finish last in the group.
Their 2002 and 2006 campaigns were both stopped by Mali in the qualifying stages. Morocco had been seeded into the second qualifying round, but two goalless draws in Bamako and Rabat sent the tie into a penalty shoot-out which Mali won 5–4. In 2004, Morocco did not enter, while a 1–6 aggregate defeat to Mali sent them out of the 2006 African Championship and the 2007 World Cup.