The 100-year-old Second World War veteran will travel to the historic royal residence in Berkshire with members of his family for the special outdoor investiture.
Captain Sir Tom raised almost £33 million for health service charities by walking 100 laps of his Bedfordshire garden.
He won the hearts of the nation for his determination, sparking a flood of donations after originally setting out to raise just £1,000.
Royal investitures were put on hold during the coronavirus pandemic and those scheduled to take place at Buckingham Palace and the Palace of Holyroodhouse in Edinburgh in June and July were postponed.
But the 94-year-old Queen, who has been staying at Windsor since before lockdown for her safety, will carry out the official engagement in person - a rare move for the monarch during the Covid-19 crisis - making a special exception to honour Captain Sir Tom.
A Buckingham Palace spokeswoman said: “On occasion the Queen invests individuals privately during audiences.
“Captain Sir Tom Moore’s knighthood was, exceptionally, announced individually by the Prime Minister, outside of the usual announcements of the Queen’s birthday honours and the New Year honours.
“Captain Sir Tom and his family were hopeful the investiture could take place in a timely fashion and we are pleased it has been possible on this occasion.”
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