The demand for US troops to exit came after French soldiers were also given their marching orders last year by Niger's new ruling generals following a July coup.
Niger announced in March it was ending a military cooperation agreement with Washington, claiming the presence of US soldiers was now "illegal".
The country has been a key base for counter-terrorism operations in West Africa, with a major US drone base near the northern city of Agadez that cost a reported $100 million to build.