The Golden Eaglets failed to clinch the bronze medal at the CAF U-17 Championship, after they were beaten 3-1 by Guinea on Sunday.
Victor Osimhen put Nigeria a goal up in the 28th minute, with his fourth goal of the competition, before Guinea drew level in the 34th minute, thanks to of Aboubacar Toure.
Abdoulaye Jules Keita then scored twice in the 39th and 53rd minute to kill off the game.
Both teams had played out a 1-1 draw, when they met in the group phase of the competition.
However, the Eaglets, alongside Guinea, South Africa and Mali will represent the continent at the FIFA U-17 World Cup in Chile this October.