King Charles, the Duke of York, the Princess Royal and the Earl of Wessex took their places around the casket four days after they participated in a vigil at St Giles' Cathedral in Edinburgh.
Other members of the royal family, including the queen consort, Vice Admiral Sir Tim Laurence, the Countess of Wessex and some of the queen's grandchildren, looked on.
All were dressed in uniform — with an exception made for the disgraced Duke of York, who is no longer a working royal — as a “special mark of respect” for the queen.
The late monarch has been lying in state in London since Wednesday and thousands of mourners have filed past to pay their final respects after queuing for hours.
On Saturday, the queen's grandchildren will participate in a vigil at her coffin and the Duke of Sussex will join his brother the Prince of Wales in wearing uniform.
Royal sources said the decision to allow Prince Harry to wear his uniform during the vigil was made by his father.
The estranged duke, who saw action on the front line during two tours of duty in Afghanistan, had been denied the chance to wear his military uniform as he publicly mourns because he is no longer a working royal.
Despite being a former army officer, he has been in civilian dress for official events, including walking behind his grandmother's coffin on Wednesday when it was carried to Westminster Hall.
The other grandchildren will be in morning coat and dark formal dress with decorations.
A royal source said Prince William will stand at the head of the coffin during the vigil while his younger brother will stand at the foot.
The source said the grandchildren, at the king's invitation, were keen to pay their respects as their parents did on Friday evening.