The Queen will be sending a message of condolence to Stephen Hawking's family, Buckingham Palace said.
The monarch met the renowned British physicist, who has died at the age of 76, on several occasions.
Professor Hawking and his daughter Lucy were introduced to the Queen in the Music Room at Buckingham Palace in 2006, at a "grey power" reception for those "Serving Beyond Sixty".
Asked afterwards if he had discussed his scientific theories with the Queen, Prof Hawking said: "I think she has other things to think about."
Questioned about grey power, he added: "I think age doesn't matter. I don't feel grey."
The same year, the Queen invited the scientist to a Buckingham Palace reception for representatives of the British scientific community.
They also encountered one another at the RHS Chelsea Flower Show, at the Royal Hospital, Chelsea, London in 2010.
In 2014, the pair met again with the Duke of Edinburgh during a reception for Leonard Cheshire Disability in the State Rooms, St James's Palace.