Born in Tema, Yakubu joined AFC Ajax at only 17, going on to remain in the Netherlands for one full decade. He made his Eredivisie debut on 19 April 2000, playing 50 minutes in a 1–1 away draw against FC Den Bosch and finishing his first season with only five appearances.
Yakubu played in an average of 15 league games in the following four years, helping the Amsterdam club to two national championships and the 2002 edition of the Dutch Cup. He spent the 2004–05 campaign on loan to fellow league side Vitesse.
In the ensuing off-season, Yakubu signed permanently with the Arnhem club for four years, being intermittently used during four seasons and released in the 2009 summer. In early October, he had an unsuccessful trial with German team TSV 1860 München.