Willow, who was nearly 15 years old, was suffering from a cancer-related illness and was put to sleep.
Willow enjoyed a few moments in the spotlight while loyally flanking the Queen.
Queen Elizabeth II has a long history with corgis, which dates back more than eight decades.
Britain's Queen Elizabeth II has lost the last descendant of her original corgi after 14-year-old Willow was put down at Windsor Castle on Sunday following a battle with cancer, according to United Kingdom media reports.
Queen Elizabeth II is mourning the loss of her last corgi.
Her death marks the end of an era, leaving the monarch without a corgi for the first time since 1944.
Willow was a 14th-generation descendant of Susan, who was initially gifted to the Queen when she turned 18.
The source continued: 'For many, many years she bred and raised corgis and to think that the last one has now gone is something of a milestone'. She was even photographed with her beloved dogs - including Willow - for Vanity Fair in 2016.
The queen still has Whisper, a corgi she adopted after the death of his owner, a former gamekeeper at her Sandringham estate. The Queen still has two dorgis, a mix of corgi and dachshund, but was said to be closest to Willow.
An insider told the publication the Queen is especially heart broken over the death of Willow.
Such was Queen Elilzabeth's attachment to Susan, she reportedly took the dog on honeymoon with Prince Philip in 1947.
Willow meanwhile appeared in the 2012 James Bond sketch which the Queen recorded for the London Olympics opening ceremony. She also reportedly didn't want to leave any behind when she dies. Willow, Monty and Holly had greeted the secret agent as he arrived at the palace to accept a mission from the Queen.
According to the source, the dog is now buried on the castle grounds.