It's the first time the royal couple have been involved in an official event since they decided to step back from their royal duties in early 2020.
It was unclear whether Harry and Meghan would be joining the rest of the Royal Family at all for the ceremony until Buckingham Palace announced it would only be senior working royals joining the Queen on the balcony.
The royal couple were instead invited by the Queen to join family members watching from the Major General’s Office overlooking the Horse Guards Parade for the illustrious occasion.
The Duke and Duchess of Sussex are also expected to have brought their two children Archie, three, and Lilibet, almost one, for the very public family reunion.
The room, which overlooks the Whitehall parade ground, sits above the entrance to Horse Guards and is where dignitaries usually watch if they are not involved in the parade itself.
While there are no official photos of the pair at the event, an image of Meghan wearing a navy outfit and wide-brimmed hat has been shared by Yahoo UK royal executive editor Omid Scobie, showing the 40-year-old playfully shushing two junior royals: Savannah Phillips, the daughter of Peter Phillips and Autumn Kelly, and Mia Tindall, Zara and Mike Tindall's daughter.
Another image shows Meghan and Harry talking to another Royal Family member.
Prince Harry and Duchess Meghan were photographed at the Major General’s Office, Horse Guards Parade earlier. The couple were seen chatting with the Duke of Kent, and Meghan was spotted playing with Savannah Philips, Mia and Lena Tindall.
📷: Kelvin Bruce/Jim Bennett pic.twitter.com/MULet9QWpl
— Omid Scobie (@scobie) June 2, 2022
A number of other senior royals, excluding Prince Andrew, were involved in the carriage procession ahead of the Trooping the Colour.
The Duchess of Cambridge, and her three children, Prince George, Princess Charlotte, and Prince Louis, accompanied the Duchess of Cornwall in the first carriage, following by the four Wessexes in the second.
The Duke and Duchess of Gloucester were in the third carriage, accompanied by Vice Admiral Sir Tim Laurence. Three horses brought up the rear, ridden by Prince Charles, Prince William and Princess Anne.
Meghan and Harry are thought to be staying at Frogmore Cottage, their home in Windsor, throughout the duration of their stay in the UK. Their permanent home is now in California.
It's expected that they'll introduce the Queen to their daughter, Lilibet, on her first birthday on Saturday.
Prince Harry hasn't visited the UK since July 2021 when he attended an engagement with Prince William to unveil a statue of their mother in London.
Watch: Harry and Meghan are attending Trooping the Colour - but not from the Balcony at Buckingham Palace