The jeering started when the Duke of Cambridge, who is the president of the Football Association, was introduced to fans during the pre-match BBC television coverage.
Some fans in the stadium also seemed to take umbrage with the national anthem and a rendition of Christian hymn Abide With Me, which were also the targets of booing.
Liverpool were victorious in the encounter itself, eventually beating Chelsea 6-5 on penalties after a goaless 120 minutes.
The behaviour of some fans at the stadium prompeted condemnation from MPs.
Commons speaker Sir Lindsay Hoyle, told MailOnline: “I utterly condemn any fans who booed Prince William at Wembley today.
“The FA Cup final should be an occasion when we come together as a country. It should not be ruined by a minority of fans’ totally shameful behaviour. In this year of all years – the Queen’s Platinum Jubilee – this is dreadful.”
And Sir Ed Davey, leader of the Liberal Democrats said: “We have the most wonderful Monarch and those fans who booed do not represent their clubs or our country.”
The Duke of Cambridge seemed unruffled by the earlier booing and handed the FA Cup trophy to a jubilant Liverpool after their win against Chelsea at Wembley Stadium.
Manager Jurgen Klopp’s side beat Chelsea 6-5 on penalties after a goalless 120 minutes on Saturday.
William gave the cup, adorned with red ribbons, to Liverpool captain Jordan Henderson from the royal box as fans cheered. He attended the match after he personally made podcast host Deborah James a dame.
The duke visited the 40-year-old, known online as Bowel Babe, at her family home in Surrey to hand over the honour for her “tireless campaigning” to raise awareness of bowel cancer.
Dame Deborah posted pictures of William with herself and her family on Instagram and said the visit gave her family “so much to smile about in the sadness”.
Additional reporting by PA