The Carrier Strike Group is in the Pacific Ocean for the first time.
The fleet, spearheaded by HMS Queen Elizabeth, has travelled through the Luzon Strait into the Phillippine Sea.
Commodore Steve Moorhouse, Commander of the Carrier Strike Group, said on Twitter: "This is a significant moment for #CSG21.
"Having begun our deployment in the Eastern Atlantic and Mediterranean, we have now travelled 10,000 miles to the Western Pacific.
"The past few weeks provided the first opportunity for HMS Queen Elizabeth to conduct blue water carrier operations.
"It means we can offer our allies and partners in the region a credible Carrier Strike Group: trained, proven and ready to contribute to maritime security."
The Carrier Strike Group recently completed exercises with the Indian, Malaysian and Thai navies before entering the contested waterway.
Upon its arrival in the South China Sea, China warned the Strike Group "it is ready to deal with 'improper acts'".
The UK's Carrier Strike Group also carried out a double replenishment at sea (RAS) – as F-35 jets took off from, and landed on, HMS Queen Elizabeth.
RFA Tidespring and Dutch naval ship HNLMS Evertsen completed the replenishment alongside the carrier as the ships, currently on the Carrier Strike Group (CSG) 21 deployment, sailed through the disputed waters of the South China Sea.
Cover image: A library picture of the UK Carrier Strike Group in convoy as it transited through the Suez Canal earlier in their journey (Picture: MOD).