Ecuadorans will decide in a referendum on November 16 whether to repeal a 2008 constitutional ban on their country hosting foreign military bases, as sought by Noboa.
Noboa told Radio Centro station that Baltra, a small island in the Pacific archipelago chain where British scientist Charles Darwin developed his theory of evolution, could be used to combat drug and fuel trafficking, as well as illegal fishing.
Baltra, which has an airport, was home to a US military base during World War II.
His remarks comes as the United States ratchets up strikes on alleged drug-smuggling boats off South America, which initially chiefly hit Venezuelan vessels but has also targeted Colombian boats.
On Tuesday, Defense Secretary Pete Hegseth announced strikes on a four more boats, killing 14 people, bringing the death toll from Washington's campaign to at least 57 since September.
Noboa did not specify which country could establish a military base in Ecuador, a major hub for cocaine trafficking, but has talked of "various countries," including the United States.
On a visit to Quito in September US Secretary of State Marco Rubio vowed to help him "wage war" against drug-trafficking "terrorists."
Noboa said Tuesday hosting foreign troops in the Galapagos "is not to harm the Galapagos or to give them away, it is to protect them."
The Galapagos Islands, a World Heritage Site, are situated some 1,000 kilometers (620 miles) off the coast of Ecuador.
The Ecuadoran armed forces regularly seize drugs, weapons, and fuel in the surrounding waters.
The United States for years operated a military base in Ecuador's Pacific port of Manta.
In 2009, then left-wing president Rafael Correa, a fierce US critic, refused to renew the lease.
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