All American soldiers are scheduled to leave Niger, ending their role in the fight against the Islamist rebels.
Military leaders in the West African country have been seeking closer ties with Russia since seizing power in a coup last year.
The United States also announced on Friday that it had agreed to close the drone base near Agadez in the Sahara Desert.
Niger is located in the Sahel region of Africa, which is considered the new global center for ISIS.
The United States has relied on Niger as a primary base for monitoring regional jihadist activity.
An American delegation is scheduled to head within days to Niamey, the capital of Niger, to arrange an orderly withdrawal of its forces, which number more than 1,000 soldiers.
Friday's announcement came after talks in Washington between US Deputy Secretary of State Kurt Campbell and Nigerien Prime Minister Ali Mahamane Lamine Zein.
The $100m (£80m) US military base there was built just six years ago and has played a key role in the US and French strategy to fight jihadists in West Africa.
But Niger's relations with the two Western countries became strained last year in the wake of the coup, and military leaders sought closer security relations with Russia.
Dozens of Russian military trainers have arrived in Niger in recent weeks, bringing with them an advanced air defense system, according to state media reports.
Niger has also distanced itself from local democracies and sought stronger regional alliances with the junta-led states of Burkina Faso and Mali.
The trio withdrew from ECOWAS, the West African regional body that opposed their military takeover.
They also withdrew from the French-backed G5 Sahel force, saying it was ineffective and undermining African sovereignty, and launched their own defense pact called the Sahel Alliance.
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