Hopes were high following a strong performance at Saratoga last month, but things fell apart at York where Golden Pal trailed off badly despite initially leading after some exceptional early speed. He finished in seventh place, five lengths behind winner Winter Power.
Trainer Wesley Ward had been hoping for his first success in the Nunthorpe, with Acapulco finishing second in 2015 and Lady Aurelia a runner-up two years later.
Golden Pal won the Breeders' Cup Juvenile Turf Sprint at Keeneland in 2020, with another performance at the showpiece meeting now the target.
"He came home safe and sound and is back here training at Keeneland like he never left," said Ward.
"Every trainer is different, but historically for me, when I bring a horse back from a long lay-off and they run a big race like he did at Saratoga, they need a little bit more time before they run again.
"I knew how important the Nunthorpe was to the Coolmore team for his stallion career, as opposed to the Flying Five (at the Curragh in September), so I factored that in and there was no real reason not to run, with the exception of the time factor.
"Every horse is different and this horse trained beautiful going into it and came out of the race beautiful, so I think it was just a question of it kind of zapped him from the inside, that first big race he had (at Saratoga)."
Golden Pal is likely to have one more run before heading to Del Mar for the Breeders' Cup.
Ward added: "We'll make a decision on whether we run him in the Woodford here at Keeneland (October 9) and then aim for the Breeders' Cup - I think that will be the plan.
"Hopefully he can run right here on his home track and he'll bounce forward right into the Breeders' Cup and show what he is."