The statement said the withdrawal would not affect the continuation of US-Niger relations.
“The United States and Niger are committed to ongoing diplomatic dialogue to define the future of their bilateral relations,” it read.
The deal was reached after marathon talks between the two countries in Niamey.
In March, Niger announced the end of its military agreement with the US. Military spokesperson Col Amadou Abdramane accused the US of raising objections about the allies that Niger had chosen.
Col Abdramane condemned the US for its “condescending attitude” and “threat of reprisals”.
Tensions spiked between the US and Niger after elected president, Mohamed Bazoum, was overthrown last year.
Niger is in Africa’s Sahel region, considered the new global epicentre of the Islamic State group.
American forces have used two military bases in Niger to monitor Islamist militant groups in the Sahel.