The Nimitz-class vessel's port call came the same day that China's first domestically produced aircraft carrier, the Shandong, sailed into Hong Kong.
Beijing claims almost the entirety of the South China Sea, through which more than 60 percent of global maritime trade passes, despite an international ruling its assertion has no merit.
"The US Navy along with our allies and partners are committed to a free and open Indo-Pacific," the ship's spokesman, Lieutenant-Commander Mark Langford, told AFP by email, without offering further details about the visit.
"These operations demonstrate the commitment to stability in the region, a commitment we uphold throughout the year and regardless of current events," Langford said, calling the Philippines a "long-standing and critical ally".
Manila and Washington have deepened their cooperation since President Ferdinand Marcos took office in 2022 and began pushing back on Beijing's South China Sea claims.
Bound by a 1951 mutual defence treaty, the two allies conduct frequent maritime exercises in the South China Sea. The Philippine and US coast guards in May conducted their first-ever joint military drills in the archipelago nation's coastal waters.
The Shandong, which sailed off the northern Philippines in April, arrived in Hong Kong on Thursday after concluding combat drills in the western Pacific alongside fellow Chinese aircraft carrier the Liaoning.
The US Department of Defense said in a December report that China numerically has the largest navy in the world, with a battle force of more than 370 ships and submarines.
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