The queen, who wore a pastel blue outfit, rode in a vintage horse-drawn carriage with her husband Prince Philip, starting from Buckingham Palace. She then inspected more than 1,000 soldiers at Horse Guards Parade.
"Trooping the Color" originated from traditional preparations for battle, when flags were carried or "trooped" down the ranks for soldiers to see.
The queen turned 88 on April 21, her actual birth date, which is usually celebrated in private. The monarch traditionally marks her birthday publicly in June.
Other senior royals also turned out for the ceremony: Prince William and his father, Prince Charles, rode on horseback. The Duchess of Cambridge, William's wife Kate, rode in a carriage with Charles' wife Camilla, the Duchess of Cornwall, but left her baby boy George at home.
A huge crowd later gathered at Buckingham Palace, where the royal family appeared together on the balcony to watch a ceremonial Royal Air Force fly-past.