Ben Pauling's stable star was unable to be saved despite intensive treatment and surgery.
The gelding, who was owned by Paul and Clare Rooney, gave Pauling his first Cheltenham Festival winner in 2017 when landing the Grade 1 Neptune Novices' Hurdle.
He was also a Grade 2 winner over fences, but he had been off the track since January last year following a number of setbacks.
A statement on Ben Pauling's website said: "It is with a heavy heart that we have to report the loss of the wonderful Willoughby Court after he lost his battle against an infection that unfortunately ended up becoming so ingrained in his sesamoid bone that sadly after many attempts he could not be saved.
"He has left a huge hole in our yard and it is a dreadful blow for all of us at Ben Pauling Racing and his brilliant owners Paul and Clare Rooney, who along with Jason Maguire have made the last few months and this time a lot easier.
"We cannot thank them enough for their support and the lengths they went to in order to try and save him. No stone was left unturned and our thoughts are with them.
"Our star has bowed out too soon but he has left us with memories that will last a life time and given us days we could have only of dreamt of.
"A horse that had everything you look for in a top class racehorse and a heart to match.
"Very sadly this exceptionally talented horse will never have the opportunity to shine bright for many years to come. He is irreplaceable."
Willoughby Court won seven of his 11 career starts, winning £135,064 in prize money.
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