Willow had an illness which was "cancer related" and it's reported that The Queen made the hard decision to have her companion put to sleep so that the almost 15-year-old dog would not suffer.
Whisper died in Windsor and while the cause of death is unknown, many Corgis die from cancer-related illnesses.
"Whisper was a friendly chap and followed her everywhere", says a source.
The queen had taken the pup under her wing after its former owner, Bill Fenwick, died in 2016.
Queen Elizabeth also has two dorgis - dachshund and corgi crosses - named Candy and Vulcan.
Whisper is the second corgi Her Majesty has lost this year as her beloved Willow passed away in April. "The Queen thought it was a bit obscure and preferred the proper spelling".More news: 'Car crash in slow motion': Aussies crushed by Pakistan
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The legacy of Queen Elizabeth's corgis may have come to an end, but the public can relive it through a forthcoming animated film, "The Queen's Corgi". Nancy, his late wife, was in charge of taking care of the monarch's group of dogs while she was away on her travels and royal engagements.
Willow was the 14th generation of Corgi in the royal family, as the then Princess Elizabeth was given Susan as an 18th birthday present.
"She couldn't resist Whisper and now she has asked Bill's family if she can keep him", a source told The Sun previous year.
The Queen's corgis were said to have ruled the roost in Buckingham Palace and according to the Independent, they were served fish, steak, rabbit or chicken for dinner.
All her subsequent corgis - apart from Whisper - can trace their lineage back to Susan, and the Queen became an expert on the breed. It is probably because Willow was the last link to her parents and a pastime that goes back to her own childhood. Follow Yahoo Lifestyle on Facebook, Twitter and Instagram.