US warships periodically conduct navigation exercises in the strait, often triggering angry responses from China which claims Taiwan as part of its territory.
Beijing views any ships passing through the strait as essentially a breach of its sovereignty – while the US and many other nations view the route as international waters open to all.
The voyage by the USS John S McCain “demonstrates the US commitment to a free and open Indo-Pacific”, the Seventh Fleet statement said.
“The United States military will continue to fly, sail and operate anywhere international law allows.”
Taiwan’s defence ministry confirmed the journey without identifying the vessel.
Beijing ‘monitoring situation’
Beijing on Thursday said it was “closely monitoring” the situation.
Foreign ministry spokesman Wang Wenbin said China would “continue to be on high alert at all times, respond to all threats and provocations at any moment, and will resolutely safeguard its sovereignty and territorial integrity”.
The transit comes after two US reconnaissance planes and one jet tanker flew near Taiwan’s airspace on Monday, according to the island’s defence ministry, which did not disclose their routes.
Beijing has stepped up military, diplomatic and economic pressure on the island since the election of President Tsai Ing-wen in 2016, as she refuses to acknowledge Beijing’s stance that the island is part of “one China”.
Last year Chinese military jets made a record 380 incursions into Taiwan’s defence zone, with some analysts warning tensions between the two sides were at their highest since the mid-1990s.