Admiral Scott Swift, commander of the US Pacific Fleet, confirmed at a press roundtable in Seoul on Monday that he had been aboard the seven-hour flight of a Boeing P-8 surveillance plane, but gave no specific details about the flight.
In May, Beijing called a P-8 surveillance flight carrying a CNN team over the South China Sea "irresponsible and dangerous".
Swift said his flight was routine, like the earlier CNN flight, and did not say if China responded to Saturday's patrol.
China's defense and foreign ministries did not immediately respond to a request for comment.
"We have forces deployed throughout the region to demonstrate the United States commitment to freedom of navigation," said Swift, adding the flight allowed him to see "first-hand" new operational capabilities in the fleet.
Swift said communications with China at sea were "positive and structured". "They're normalized, if you will," he said.
China has almost finished building a 3,000-metre-long (10,000-foot) airstrip on one of its artificial islands in the disputed Spratly archipelago of the South China Sea, according to satellite imagery of the area.
Beijing claims most of the South China Sea, with the Philippines, Vietnam, Malaysia and others holding overlapping claims.
Washington has demanded China halt land reclamation and militarization of the disputed area and to pursue a peaceful resolution according to international law.
China stepped up its creation of artificial islands last year, alarming several countries in Asia and drawing criticism from Washington.
Beijing says the outposts will have undefined military purposes, as well as help with maritime search and rescue, disaster relief and navigation, Reuters reported.