Manu Garba who named a 20 man squad for the competition reportedly had to make do without his skipper who was sidelined.
The Golden Eaglets struggled in the encounter against Burkina Faso as they feel behind to two quick opening goals.
The WAFU Zone B U-17 AFCON qualifiers is hosted by Niger Republic and the Golden Eaglets fell behind through goals by Albert Outtara and Issa Ouedrago after just six minutes in the encounter.
The players however rallied themselves back into the encounter first with Samson Tijani and before the end of the first half Olakunle Olusegun equalised to restore parity in the encounter.
Both sides aimed for the winning goal in the second half but it was Burkina Faso who would get it in the 79th minute as they held on for all three points in their group opener.
Manu Garba's team face a difficult task to advance from the group and must win their other two group games after a defeat in their opener.
Their second group game will be against Cote d’Ivoire on Thursday, August 6 and will finish their group campaign against Benin Republic on Sunday, August 9.