Her family gathered at her Scottish estate after concerns grew about her health earlier on Thursday.
The Queen came to the throne in 1952 and witnessed enormous social change.
With her death, her eldest son Charles, the former Prince of Wales, will lead the country in mourning as the new King and head of state for 14 Commonwealth realms.
In a statement, Buckingham Palace said: “The Queen died peacefully at Balmoral this afternoon. “The King and the Queen Consort will remain at Balmoral this evening and will return to London tomorrow.”
All the Queen’s children travelled to Balmoral, near Aberdeen, after doctors placed the Queen under medical supervision. Her grandson, Prince William, is also there, with his brother, Prince Harry, on his way.