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, His Majesty the King said: “The death of my beloved mother Her Majesty the Queen, is a moment of the greatest sadness for me and all members of my family.
“We mourn profoundly the passing of a cherished Sovereign and a much-loved Mother. I know her loss will be deeply felt throughout the country, the Realms and the Commonwealth, and by countless people around the world.”
He said during the period of mourning and change he and his family would be “comforted and sustained by our knowledge of the respect and deep affection in which The Queen was so widely held”.
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.
