An infection in his joint prevented the 2017 Cheltenham Festival winner from making his comeback in November, but all had been going to plan with his recuperation until the same problem flared up once more.
Pauling said: “Unfortunately, the infection in the bone had flared up again and despite the best efforts of the fantastic team at Bourton Vale Equine Clinic, sadly we had no alternative but to put him down.
“Willoughby was a huge character around the yard. His brilliance was that he was that bit different and that bit sharper than any other horse I have ever trained.
“He was a fabulous jumper who very quickly became an incredibly tough competitor which was proven in many of his races, none more so than when he won the Neptune at Cheltenham.”
Willoughby Court was a gutsy winner of the Neptune Investment Management Novices’ Hurdle at the Festival, proving Pauling and the Rooneys with a moment to cherish at the showpiece meeting.
Pauling continued in a statement: “Being our first Festival winner will mean he’ll always be very fondly remembered.
“Frustratingly, he never actually had many races and we all felt that there was a huge amount of improvement to come.
“Paul and Clare Rooney have been huge supporters of mine from a very early stage in my career and Willoughby was the first store horse they ever bought.
“They’ve been a huge support in every way possible for both Willoughby and the team back at home, and I really can’t thank them and Jason Maguire (racing manager) enough.
“We did everything we possibly could to save him, as even if he had never made the track again, Paul and Clare would have been delighted just to have him at home.
“Unfortunately, it just wasn’t to be despite everything that Bourton Vale Equine Clinic, Donnington Grove Vets and Graham Potts did to save him. He will be sorely missed by us all.”