The Earl of Wessex and Princess Anne were part of the 400-person strong congregation that collected at Saint George's Chapel in the castle grounds, the BBC reported Sunday.
The queen, who came dressed in a flowing raspberry coat and maroon hat with a pink silk flower, made sure to wave to her fans before entering the castle.
The traditional ceremony was led by the Rt. Rev. David Connor, the dean of Windsor.
The Lower Ward of Windsor Castle is where the 15th century Gothic chapel and final resting place of Henry VIII, Charles I and George VI, is located. The Queen Mother and Princess Margaret are also buried there.
Also, the Duchess of Cornwall appeared for the first time since her hysterectomy operation. She joined her husband, the Prince of Wales, at Crathie Kirk on Royal Deeside in Scotland for an Easter Sunday service.