Her Late Majesty is buried alongside her late husband, the Duke of Edinburgh, within the King George VI Memorial Chapel.
HELLO! understands that other members of the royal family have paid their respects privately at the chapel on Friday morning.
Meanwhile, the King and Queen attended a private church service at Crathie Kirk near to the Balmoral estate.
Charles and Camilla were joined by the King's cousins, Lady Sarah Chatto and the 2nd Earl of Snowdon.
Harry's appearance comes after he paid tribute to his late grandmother during his speech at the WellChild Awards in London on Thursday evening.
At the ceremony, the Duke reflected on the events of 12 months ago when he was forced to miss the awards as he rushed to Balmoral in Aberdeenshire after the Queen was taken ill.
He said: "As you know, I was unable to attend the awards last year as my grandmother passed away.
"As you also probably know, she would have been the first person to insist that I still come to be with you all instead of going to her, and that’s precisely why I know exactly one year on that she is looking down on all of us tonight, happy we’re together, continuing to spotlight such an incredible community."
Harry is set to travel to Germany for the opening ceremony of the Invictus Games Dusseldorf on Saturday.
The Duchess of Sussex will fly from California to join her husband at the Games shortly after the tournament begins.
In the first episode of HELLO!'s A Right Royal Podcast, writer and broadcaster Gyles Brandreth and photographer Julian Calder share their favourite memoires of the late Queen. Listen here...