Twelve-year-old Whisper had become a royal favourite following the death earlier this year of Willow - the last corgi she reared herself.
He died last Corgi of Queen Elizabeth II.
Whisper contracted an illness a few weeks ago and died this week, The Daily Mail reports.
Whisper, aged 12, followed the Queen from room to room and accompanied her to meetings with dignitaries.
"The Queen has quickly become very attached to the dog", added the source.
The Queen took care of Corgi in 2016 after the death of her previous owner - a huntsman in the Royal residence of Sandringham bill Fenwick.
The British monarch has two dogs remaining, "dorgis" (corgi-daschund crosses) Candy and Vulcan. "The Queen thought it was a bit obscure and preferred the proper spelling".
"The Fenwicks looked after their corgis like the Queen did so she knew there would be no problem if Whisper came to the Palace".
She took them everywhere.
The Queen was given her first dog, a Cairn terrier, at the age of three by her uncle, the Prince of Wales.
"She couldn't resist Whisper and now she has asked Bill's family if she can keep him", a source told The Sun a year ago.
The Queen's pampered pooches were known to have their own room in Buckingham Palace, sleeping in elevated wicker baskets.
According to the Mail, the Queen made a decision to stop breeding corgis five years ago over fears she could trip over an excitable puppy, adding to her concerns over who would take care of them when she was no longer around.
The Queen was frequently pictured surrounded by corgis, and her love for the breed is legendary.