Babangida joined Ajax in the summer of 1996 in a long-anticipated €5 million move. He appeared in 29 league games, scoring four goals in his first season with Ajax. Babangida played an important role in Ajax's European campaign, scoring three goals, including one against Auxerre in the group stages, and the winning goal in the second leg of the UEFA Champions League encounter with Atlético Madrid at the Vicente Calderón Stadium, that put Ajax through to the semi-finals of the competition.