The USS Dewey traveled within 12 nautical miles of the Mischief Reef in the Spratly Islands, several US officials speaking on condition of anonymity said on Wednesday.
The so-called freedom of navigation operation, which is sure to anger China, is the first such challenge to Beijing in the strategic waterway since Trump took office.
Territorial waters are generally defined by a United Nations convention as extending 12 nautical miles from a country’s coastline.
China has repeatedly warned the United States against any military activities in the South China Sea.
Trump blasted Beijing during the 2016 presidential campaign for militarizing parts of the South China Sea, stealing American jobs with unfair trade policies and manipulating its currency in its favor.
The US operation was the first of its kind since October, which was approved by then-President Barack Obama. Under the previous administration, the U.S Navy conducted several such voyages through the South China Sea.
Washington says Beijing seeks to limit freedom of navigation in the disputed waters.
The operation comes as Washington has called on Beijing to cooperate in curbing North Korea's nuclear and missile programs.
Trump hosted Chinese President Xi Jinping for a summit at his Florida resort last month. During the meeting, Trump praised the Chinese president for efforts to restrain North Korea.
The US Defense Department gave no details of the latest mission but said in a statement it was continuing regular freedom of navigation operations and would do more in the future.
"We operate in the Asia-Pacific region on a daily basis, including in the South China Sea. We operate in accordance with international law," Pentagon spokesman Captain Jeff Davis said in the statement.
China says the United States is meddling in regional disputes and is deliberately escalating the situation in the waters.
The South China Sea is the subject of a territorial dispute between China and Vietnam, Taiwan, the Philippines, Malaysia, and Brunei. But those countries seem to have been managing their disputes with China smoothly.