The patrol, known as a freedom of navigation operation, was conducted Wednesday around Mischief Reef, one of a chain of disputed islands in the South China Sea. The guided-missile destroyer USS Dewey conducted the patrol, according to U.S. officials.

A freedom of navigation patrol, known in military parlance as a Fonop, represents a challenge to excessive maritime claims. Such operations must take place within 12 nautical miles of an island or feature’s territorial waters to legally constitute a freedom of navigation patrol.

The patrol Wednesday was the first since October, and the first since Mr. Trump took office in January.

Capt. Jeff Davis, a Pentagon spokesman, declined to comment on the operation. “We operate in the Asia-Pacific region on a daily basis, including in the South China Sea,” he said in a statement. “We operate in accordance with international law.” He added that the patrols are “not about any one country, or any one body of water.”

The president has sent mixed signals to Beijing. Mr. Trump’s presidential campaign blamed the Obama administration for claims by China to disputed areas in the South China Sea and for allowing Beijing to construct military facilities, including runways, hangars and ports.

Once in office, Mr. Trump turned to Chinese President Xi Jinping for help in constraining North Korea’s advancing nuclear weapons program.

Adm. Harry Harris, who heads U.S. Pacific Command and who has been a vocal proponent of conducting more freedom of navigation patrols, told a House panel April 26 “I think we’ll be doing some soon.”

But as many as three requests to conduct Fonops since Mr. Trump took office were rejected by officials as Mr. Trump cultivated ties with China, according to U.S. officials. The rejections were first reported by the New York Times .

Earlier this month, Adm. Harris visited a Japanese radar station on an island in the East China Sea, the site of a territorial dispute between Japan and China, signaling the U.S. commander’s intention to press China on such disputes. In the little-noticed visit, Adm. Harris touched down at the Yonaguni Coast Observation Unit, an intelligence-gathering facility, on an island in the Ryukyu Islands with Adm. Katsutoshi Kawano, the chief of staff of Japan’s self-defense force, officials said.

In the overlapping territorial disputes of the South China Sea, the U.S. isn’t a claimant and supports a multilateral process for sorting out claims. Meanwhile, U.S. officials have said they maintain an interest in keeping sea lanes open to the passage of hundreds of millions of dollars in annual shipping.

Conducting freedom of navigation operations in the South China Sea has long been controversial. Inside the Pentagon, officials have debated how often they should be conducted—and to what extent they should be announced publicly.

Some defense officials believe such patrols should be kept private so as not to shame Beijing, but at the same time send a quiet message to China. Others believe the U.S. should talk about them publicly to signal its intentions to allies and to China. Still other U.S. officials believe that if the U.S. begins to conduct more routine patrols, then public and media interest would wane as they will become a more routine matter, U.S. officials said.

The last navigation patrol was conducted Oct. 21. Others were conducted in October 2015, January 2016 and May 2016, according to the Center for Strategic and International Studies, a Washington think tank that has tracked the patrols.