Waddington will be the main operating base for the aircraft and is already responsible for operating the Reaper aircraft.
Speaking at RIAT, Gavin Williamson said: "The Royal International Air Tattoo is a perfect example of how Britain continues to lead the way in airpower, showing the story from the historic Lancaster, to the stealthy F-35 Lightning and now the incredible arrival of the Protector.
"Today’s show embodies how our RAF continue to have the equipment they need to protect our country and our interests around the world."
The RAF paraded their new centenary colours at RIAT
In a historic first, the aircraft flew non-stop from North Dakota, US to Gloucestershire in a flight that took over just over 20 hours, making it the first Medium Altitude Long Endurance Remotely Piloted Air System (RPAS) to transit across the Atlantic.
The aircraft will contribute to Homeland and Defence tasks including military aid to civil authorities, armed intelligence, surveillance, reconnaissance and target acquisition until beyond the mid-2030s.
The Protector aircraft will be based at RAF Waddington, with planned investment of £93 million to construct a new purpose-built hanger as well new facilities and accommodation for crews.
The Protector is also the world’s first RPAS to be designed, built and certified against stringent NATO and UK safety standards – meaning it can operate over populate areas.
The Defence Secretary also presented two British pilots with 1,000 flying hour certificates after they reached the milestone in the submarine-hunting P8-A Poseidon Maritime Patrol Aircraft being purchased by the UK.
Squadron Leaders Mark Faulds and Ian Tuff reached the achievement as part of their time training in the Seedcorn crew with the United States Navy.
The UK has ordered nine of the aircraft, investing £3 billion over the next decade in its Maritime Patrol Capability.