Dressed in a purple hat and matching long coat, Her Majesty also unveiled a plaque at the museum in Windsor's Guildhall commemorating her visit to the historical venue.
A schoolgirl beamed with joy as she handed flowers to the Queen who officially opened the museum.
The Queen was welcomed by hundreds of supporters who lined the High Street to greet her on the second stop of her visit to Windsor. She was shown around the museum with staff and volunteers on hand to explain artefacts and exhibits.
Museum assistant Amelia Evans, who was demonstrating a workshop on the Olympic Games, said: "I think she chose to come because Windsor is her home and it’s very important to her.
"I was very nervous to speak to her, but she puts you at ease. I showed her a medal from the 1908 Olympics and she held it and said the new ones are heavy too."
She then went to unveil the light blue oval plaque in the Ascot Room – where Prince Charles and Camilla married in 2005.
Here the Queen met a handful of guests including Royal Borough councillors, Mayor Cllr Asghar Majeed, and chief constable of Thames Valley Police, Sara Thornton.
On her way out, she was welcomed by the waving of dozens of flags from year four pupils at The Queen Anne Royal Free First School.
Pupil Natasha Goldsworthy, nine, smiled from ear to ear as she gave the Queen the posy of flowers and said she couldn't believe she was picked.
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Trains travelling to and from London Paddington are facing 'major disruption' this afternoon, with some services set to be delayed by up to an hour, cancelled or revised.