Yakubu made his full international debut on 22 April 2000 in a 4–0 home win in Lagos against Eritrea in qualification for the 2002 African Cup of Nations. He scored his first international goal in an away win against Namibia on 16 June 2001 in the same qualification campaign. On 1 July 2001, he scored his first international brace, with the second and fourth goals in a 4–0 away win over Sudan in the 2002 FIFA World Cup qualification stage. He was named in the squad for the 2002 Africa Cup of Nations in Mali and was given the number 8 shirt by manager Shuaibu Amodu. On 9 February 2002, Yakubu scored the only goal of the third-place play-off against Mali after 29 minutes. However, Yakubu was not named later in the year in the squad selected by new manager Festus Onigbinde for the 2002 World Cup in Japan and South Korea.