The Golden Eaglets threatened early through Lawrence Abuchi threatened, but it was the Junior Menas who took the lead through Abdoul Razaq Zada in the 20th minute.
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Columbus Igboenyobe attempted to restore parity before half-time, but his effort was comfortably saved.
Despite changes made by coach Eboboritse Uwejamomere, Niger Republic doubled their advantage in the 87th minute, leaving the five-time world champions facing defeat.
Fasiu Mubarak pulled one back in the fifth minute of stoppage time, but that could not complete the comeback for the Nigerian lads.
The Golden Eaglets will seek their first points when they face Ivory Coast in Friday’s crucial Group B encounter.