The Duke of Sussex travelled to the Highlands estate on Thursday following the death of Queen Elizabeth II.
But GB News' Cameron Walker reports that Harry left Balmoral shortly before 8.30am on Friday morning.
The Duke was seen with members of his security team, and no other member of the Royal Family.
He was later seen boarding a British Airways flight at Aberdeen International Airport. He wore a black suit and carried a shoulder bag as he walked towards the steps of the plane.
The British Airways flight landed at London Heathrow Airport at 11:32am, after completing its journey.
Harry made the trip to Scotland to see his beloved grandmother on Thursday while his wife, Meghan Markle, stayed in London.
Prince Harry was seen at Aberdeen International Airport PHIL NOBLE
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Prince Harry had visited Scotland on Thursday evening PHIL NOBLE
It comes after the tragic death of Queen Elizabeth II – news that was confirmed by Buckingham Palace at 6.30pm on Thursday.
A statement reads: “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.”
Her eldest son, Charles, 73, will now ascend the throne after being the longest-serving Prince of Wales in history.
He will be formally proclaimed monarch at a historic Accession Council this weekend.
When the meeting begins, the Lord President announces the death of the sovereign and calls upon the Clerk of the Council to read aloud the text of the Accession Proclamation.
It will include the monarch's chosen title – King Charles III.
The platform party – made up of Camilla and William, the Archbishop of Canterbury, the Lord Chancellor, the Archbishop of York, the Prime Minister, the Lord Privy Seal, the Lord Great Chamberlain, the Earl Marshal and the Lord President – sign the Proclamation.
The Lord President then calls for silence and reads the remaining items of business, which deal with the dissemination of the Proclamation and various orders giving directions for firing guns at Hyde Park and the Tower of London.
The King then enters and holds his first Council, which is only attended by Privy Counsellors.
He will first make a personal declaration about the death of Queen Elizabeth II.