The world champions were also drawn against Algeria, Libya and Gabon.
Algeria and Libya will play in the first round between June and July, before they face Gabon in the second round in August.
Nigeria will begin their Journey to the 2017 u-17 world Cup against Niger in the second round in August.
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The overall winners will then battle the winners of the clash between Nigeria and Niger in September to determine the qualifier for the tournament.
The top four teams in Madagascar will represent Africa at the 2017 u-17 World Cup in India.
Similarly, Nigeria has been drawn with the Democratic Republic of Congo, Kenya and Malawi in the qualifying rounds for Africa Under-20 Cup of Nations holding in Zambia next year.