And the USS Dewey sailed close to Mischief Reef in May.
A Navy official confirmed the operation to Fox News, saying that a US Navy P-8 reconnaissance plane flew nearby to monitor the operation, but stayed outside of the airspace claimed by China.
The so-called "freedom of navigation" mission involved the Arleigh Burke-class guided missile destroyer sailing within the 12-mile range of an artificial island reclaimed by China, Reuters reported, citing U.S. officials, speaking on condition of anonymity.
The show of USA force came as the Trump administration upped the pressure on China to bring Pyongyang to heel, just hours after North Korea threatened to target a U.S. military base on the Pacific island of Guam.
The Foreign Ministry pointed out that that the so-called United States "freedom of navigation" mission was carried out without authorization from Beijing, with has "indisputable sovereignty over the Nansha Islands (Spratley) and its surrounding waters".
China's Defense Ministry said two Chinese warships "jumped into action" and warned the US ship to leave, labelling the move a "provocation" that seriously harms mutual trust.
"At the moment the relations between the armed forces of China and the United States show stable development". Neither China's defence ministry nor its foreign ministry immediately responded to a request for comment.
"China is very displeased with this and will bring up the issue with the United States side", the statement reads.
A spokeswoman for U.S. Pacific Fleet said that all Navy operations "are conducted in accordance with worldwide law and demonstrate that the United States will fly, sail, and operate wherever global law allows".
The Trump administration has vowed to conduct more robust South China Sea operations.
The Philippines, Vietnam, Malaysia, Taiwan and Brunei have overlapping claims.
North Korea says it needs long-range ballistic missiles and nuclear warhead they could carry as deterrence against a possible American aggression.
But Washington's patrols have often angered Beijing because the United States is not a claimant in the territorial dispute in the mineral-rich South China Sea.
Experts and officials have criticised President Barack Obama for potentially reinforcing China's claims by sticking to innocent passage, in which a warship effectively recognised a territorial sea by crossing it speedily without stopping.