Mami Ueno scored a hat-trick, while Yuka Momiki scored twice for the Asians. Falconets’ Mary Ologbosere was responsible for an own goal in the encounter.
It is the second time Japan will defeat Nigeria at the U-20 World Cup, after they won as hosts in 2012.
Momiki opened scoring in the 34th minute, before Ueno doubled their advantage three minutes later. Momiki got her second in the 51st minute, before Ologbosere’s own goal made it 4-0.
Ueno then netted twice to complete her hat-trick.
In the group’s other game Spain crushed Canada 5-0.
The Falconets will take on Canada in their second group fixture on Wednesday, while Spain will play Japan.