The university plans to return the stone to the dockyard site, This Is Local London reported.
The stone, about 8 feet high, carries the initials "H" and "K" for Henry VIII and Katherine of Aragon, the first of his eight wives, ITV News reported. It was moved to the university after the dockyard site was damaged by bombing during World War II.
Deptford, a neighborhood downstream on the Thames from the ancient City of London, was once a separate village. The dockyard founded there by Henry VIII was one of his country's major naval installations through the Napoleonic Wars and a victualing yard remained there into the 1960s.
Chris Mazeika, a member of a local community group, Deptford Is, spotted the stone during a visit to the university and realized its significance. It had been concealed for decades behind a false wall.
The dockyard site is currently an ancient monument. Mayor Boris Johnson is expected to decide next month whether to allow a large development, including 3,500 homes and a hotel, to be built on the site, This Is Local London said.
"The rediscovery of the foundation stone reminds us that this site was the foremost royal dockyard of the Tudor period, and a historic site of national importance at this critical moment when its future is to be decided by the mayor of London," Jonathan Foyle, the chief executive of World Monuments Fund Britain, said.