Aleem Maqbool, Religion Editor for the BBC, revealed the personal message, which was shared whilst flying over the United Kingdom.
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The message, addressed to Her Majesty Queen Elizabeth II, read: "As I fly over the United Kingdom en route to Canada, I send greetings of good wishes to Your Majesty, the members of the royal family and all the people of the realm. I pray that Almighty God will bless you with his gifts of strength, joy and peace."
Fans loved the greeting, and quickly took to comment under Aleem's post.
The Queen and Pope Francis pictured together at The Vatican back in 2014
"How thoughtful and lovely," one wrote, whilst another added: "How very sweet."
The Queen would have received the special message in Balmoral, where she is currently enjoying her summer holidays.
The monarch travelled to her favourite residence last week and is likely to spend several months at the estate. She will no doubt be joined by other members of her family during her time there.
Her Majesty pictured during a recent visit to Thames Hospice on 15 July
The Queen usually travels to Balmoral from mid to end of July and first stays at Craigowan Lodge - the stone cottage which is located a mile from the main Balmoral Castle.
She will reside at the seven-bedroom lodge until her main Scottish residence closes to the public on 2 August. The Queen tends to stay in Scotland until September/October time before her royal duties resume.
Scotland is considered to be one of the Queen's favourite places on Earth; she and her late husband Prince Philip even spent part of their honeymoon at Birkhall hunting lodge, located on the estate, in 1947.
The Balmoral estate is where the royal family can relax away from their usual royal duties and enjoy the quieter life in the countryside.