The USS Dewey sailed within 20 km of Mischief Reef (a man-made Chinese island), in the Spratly Island chain, on Wednesday, in a "freedom of navigation operation," according to a US official.
While he didn't confirm details of this particular operation, Pentagon Spokesperson Captain Jeff Davis told CNN: "We operate in the Asia-Pacific region on a daily basis, including in the South China Sea."
China has previously described such operations as a serious breach of law and an intentional provocation.
The Pentagon said such operations were "not about any one country, or any one body of water", the CNN reported.
However, there were suggestions that the Trump administration was putting them off to avoid antagonising China.
China claims ownership of the vast majority of the South China Sea, including the Paracel and Spratly island chains, a claim disputed by numerous other countries including the Philippines and Vietnam.
Earlier in 2017, the US military had requested permission to perform a freedom of navigation operation but it was turned down by the Pentagon, as part of an effort to ease US-China relations, a US defence official told CNN.