A 16-year-old bushwalker has been found dead in a creek in the Blue Mountains National Park.

Police say he and his 17-year-old friend travelled to Leura train station on Tuesday before walking to Mount Hay to begin a three-day hike.

Just before 6pm on Tuesday the two walkers became separated and the older hiker activated his personal locator beacon.

Police launched a land and air search for the pair and the 17-year-old was winched to safety from the Acacia Flat campground in the Blue Gum Forest.

The younger walker could not be found at the time.

Police continued to search for the 16-year-old, assisted by the Blue Mountains rescue squad, PolAir, NSW Ambulance and the TOLL rescue helicopter.

The body of the missing boy was found about 1pm on Thursday in a creek in the Blue Gum Forest.

A post-mortem examination will be conducted on the 16-year-old to determine how he died.

A report will also be prepared for the coroner.