The Duke of Cambridge, who is the president of the FA, met with both sets of players ahead of kick-off.
However, audible boos could be heard as William made his way across the pitch.
The jeers seemed to increase during a rendition of FA Cup theme Abide With Me and then they increased again when God Save the Queen was sung.
It is unclear if both sets of fans were booing, though observers reported many of them came from the Liverpool fans.
It is the latest instance of Liverpool fans booing the national anthem, with several cases reported over the years.
There were also reports of supporters booing the anthem earlier this year when Liverpool played against Chelsea in the Carabao Cup final.
Prince William, who is the president of the FA, met with both sets of players ahead of kick-off
Fans took to Twitter to slam the booing.
One said: ‘Liverpool booing the National Anthem. Doing Merseyside no favours.’
Another said: ‘No allegiance to either but Liverpool can do one, their fans booing Prince William then our national anthem, what’s that about?’
A third said: ‘Liverpool fans once again booing the national anthem, disgusting fan base.’
The booing of the anthem is thought to be a tradition for Liverpool supporters, one that dates back to the 1980s.
It is thought to be linked to opposition to the Conservative government of that era, as well as anger at the fallout of the Hillsborough tragedy.
Omid Scobie, a close friend of Prince Harry and Meghan Markle, tweeted: ‘An unexpected moment at today’s #FACupFinal, where Liverpool fans booed Prince William and National Anthem. My understanding (correct me if I’m wrong, Twitter) is that it’s still felt there was an establishment cover-up over the Hillsborough disaster and getting justice for it.’
Prince William, Duke of Cambridge during The FA Cup Final match between Chelsea and Liverpool
The booing seemed to increase during a rendition of FA Cup theme Abide With Me and then again when God Save the Queen was sung
Liverpool manager Jurgen Klopp has previously been asked about the booing of the anthem from his team’s fans.
He said in 2019: ‘I don’t think I’m the right person (to ask), I know a bit about the history but it’s not for me to judge.
‘I know the Liverpool supporters are respectful. If they give that sign the reason might be a bit in the past. But I’ve nothing else to say about that.’
Liverpool ignored the furore to go on and win the match on penalties.
Prince William later gave out the medals after the match, with no more boos reported.
It is the latest bad press for the future king, after a blunderous tour of the Caribbean saw him and Kate hit by protests and public relations gaffes.
Prince William and Kate Middleton want to modernise the Royal Family after their chaotic Belize, Jamaica and the Bahamas.
This would include getting rid of bows and curtsies along with their formal titles so they would be known as simply Kate and William.
The scrutiny of their tour came to a head when Prince William released an unprecedented end-of-tour statement addressing growing republican sentiment in the three countries – acknowledging it had ‘brought into even sharper focus questions about the past and the future’.
In the wake of the criticism over the ‘colonial-era’ optics of their tour, many have called for an end to similar overseas trips by members of the royal family.
Sunday Times Royal Editor Roya Nikkhah believes the tour ignited a rethink of how the royal family plans overseas visits in the future.
Speaking on the BBC’s Radio 4 Today programme, she said: ‘I think it definitely will [spark a rethink] and to be honest I think that rethink had started before this tour got underway because I know that William thought long and hard about how to approach certain things.
‘There have obviously been a few missteps. We had that extraordinary statement from him on Saturday night setting out the fact that he takes that on the chin and he wants to sort of look at things differently.’
Prince Edward and Sophie Wessex faced similar issues on their royal tour of the Caribbean last month.