The This Morning shared a rare photograph on social media of 11-year-old daughter Belle and sons Harry, 13 and Chester, seven, as they paused for reflection outside the royal residence in central London where they also left tributes outside the gates.
Willoughby, 41, said: "Time to reflect and pay our respects… the children wrote the most beautiful words…"
The photograph shows the children from behind, standing in front of the gates to the Buckingham Palace grounds looking at a pile of floral tributes left in honour of Queen Elizabeth II.
The boys are wearing shirts and chinos, while Belle is wearing a checked woollen overcoat in primary colours. A second picture shows her placing an envelope on the pile. Her long blonde hair covers her face. She appears to be wearing a white lace dress under her coat.
Queen Elizabeth II died at the age of 96 on Thursday 8 September, having reigned for 70 years, and her son King Charles III became the new sovereign of Britain and the Commonwealth.
Willoughby and her This Morning co-host Phillip Schofield will present a special edition of the ITV daytime show on Monday at 11am, their first appearance on air since The Queen's death.
Chat shows Lorraine and Loose Women have both been pulled from the schedule as a mark of respect, as the nation continues its 10 days of official morning ahead of the funeral on Monday 19 September.
Breakfast show Good Morning Britain has been extended until 10am, and This Morning will follow.
Willoughby shares her three children with TV producer husband Dan Baldwin, who she married in 2007.
They live in a five-bedroom house in West London, not far from Buckingham Palace. The former folly, which dates back to the 1800s, has its own tower, complete with flagpole, from which the family have often flown a Union Jack flag.
The TV presenter is very private about sharing photographs of her family on social media and never shows their faces.
Back in May 2021 she shared a picture of her hands, holding her children's hands, at the end of the Bank Holiday weekend.
She captioned the photo on Instagram: "End of a beautiful bank holiday... school bags ready by the front door...bath, book and bed for this lot... and mummy too... see you in the morning."
Watch: Crowd remove plastic packaging from floral tribute to The Queen to help park keepers