A second half strike from Agor Chukwudi’s handed Emmanuel Amuneke’s boys a valuable away win at the Louis Rwagasore Stadium, Bujumbura.
After a goalless first half the Flying Eagles came into the second stronger, putting their opponents on the back foot.
The Nigerian side, dominated by the 2015 class that won the Fifa U17 World Cup in Chile broke the deadlock in the 64th – minute after a Chukwudi unleashed a powerful drive into the opponents net for Nigeria’s first and only goal of the game.
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The visitors never came close to equalizing as the Flying Eagles held on for a vital win.
The second leg holds on June 11 at the UJ Esuene Stadium, Calabar, with the winner over the two legs going on to face Sudan, for a place in the tournament in Zambia next year.
Nigeria is the current defending champions after winning the 2015 edition.