It is the first time the Red Arrows have performed over Windsor since the Diamond Jubilee in 2012.
Squadron Leader Tom Bould, who led the nine British-built Hawk aircraft formation over Windsor, said after a challenging year, it was "especially humbling" to fly the national colours at the ceremony.
"It is always a huge honour to carry out a flypast to mark Her Majesty the Queen's Official Birthday and even more so this year given the historic location and setting," he said.
The event is usually held on Horse Guards Parade in London, but a scaled back parade took place at Windsor Castle due to COVID-19.
As well as featuring 270 soldiers from several units, the event also included a massed band, 70 horses and personnel of the Household Cavalry in a more traditional Trooping the Colour.
Traditionally, the Queen's Birthday Flypast occurs over Buckingham Palace, where members of the public can see a number of RAF aircraft.
The Red Arrows' 57th display season got under way earlier this month, with a busy return to public events and air shows after a year of COVID-19 cancellations.
The RAF Aerobatic Team also performed a flyover for world leaders at the G7 summit in Cornwall.
Cover image: The Red Arrows about to conduct a flypast of Windsor Castle on the occasion of Her Majesty the Queen's Birthday (Picture: MOD).