In the course of a visit to a cathedral in Staffordshire on Monday, the King was confronted by a protester who questioned him about Prince Andrew's connections with convicted sex offender Jeffrey Epstein.
The protester demanded to know how long the monarch had been aware about his brother's relationship with Jeffrey Epstein, and also questioned whether he had asked the police to "conceal" for Prince Andrew.
Amid the protest, there were large groups of supporters and applause for the monarch, who was in Staffordshire for an ceremony.
Prince Andrew's connections with Epstein have been under intense scrutiny in recent weeks. The prince, who gave up his titles earlier this month, has strongly denied any misconduct.
"For how long have you been aware about Andrew and Jeffrey Epstein? Have you asked the authorities to cover up for Andrew?"
The King remained silent but carried on greeting fans, some of whom shouted "Long live the King". One supporter can be heard requesting him for a embrace.
Another woman outside the cathedral was also heard telling the heckler to "go away" and to "be quiet".
The scandal over the Duke of York's links to Epstein has been brought back into focus by misconduct allegations repeated in Virginia Giuffre's recently released book.
In the memoir, the accuser claims she had sex with the prince on multiple times, including once with Jeffrey Epstein and "several other minors"
Prince Andrew, who reached a out-of-court agreement with Ms Giuffre in recent years, has consistently denied any wrongdoing. In a previous interview, he told BBC Newsnight he did not recall meeting Ms Giuffre "at all", and that they "never had any sort of intimate relations."
But in recent times, new inquiries have been raised about how he is able to fund his way of life despite not being a active member of the royal family.
The disclosure that he has only ever paid a token annual rent on his Royal Lodge has intensified the scrutiny over his living arrangements - even though he made large payments up front, including for improvements.
The political party said he should be summoned front of MPs to give testimony about his rental agreement of his lodge.
But last Thursday, the government refused to give parliamentarians time to discuss the prince's status or his residence, despite increasing calls for scrutiny.
Buckingham Palace has not issued a statement on whether Prince Andrew might relocate of his home - or where he might reside.
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Thomas Richardson