Wetherspoon is to invest approximately £2.5 million developing the pub.
It is set to open in the summer.
A total of 120 full and part-time jobs will be created at the pub.
The pub will be named The Lion and the Unicorn, a reference to the Festival of Britain which was held close to the site of the pub in 1951.
One of the pavilions was named The Lion and the Unicorn.
The pub will be located on the upper ground floor of The Sidings development (a repurposing of the former Eurostar Terminal, by placemaking expert LCR).
Wetherspoon chairman and founder, Tim Martin, said: “We are looking forward to opening our new pub.
“We are confident it will appeal to a wide range of people and be a great asset to the station itself.”
LCR’s asset management director, Sian Evans, added: “The Sidings at Waterloo is set to become one of London’s leading leisure and entertainment destinations.
“The new Wetherspoon pub will provide another great reason for people to visit.”