The Duke of Edinburgh held the title for 66 years after first receiving the honour in 1954.
WATCH: Prince Charles and Camilla arrive in Rwanda for Commonwealth meeting
President of the RCSEd, Michael Griffin, said it is a "privilege" to welcome Charles, who is known as the Duke of Rothesay in Scotland, as its new patron.
He enthused: "It is a privilege to welcome HRH The Duke of Rothesay as Patron of the Royal College of Surgeons of Edinburgh.
Philip was awarded the title in 1954
"The Duke of Edinburgh played a very significant part in the College’s history during His Royal Highness’ 66 years as Patron, which we recognised in 2015 by constructing the Prince Philip Building.
"The Duke’s engagement with Fellows and officers at the opening of the building was extraordinary, and throughout his patronage His Royal Highness took great interest in the surgical profession and its advancement of patient care.
"We very much look forward to working with The Duke of Rothesay."
The royal duo took to social media
The RCSEd is one of the oldest surgical corporations in the world and awarded Philip with an honorary fellowship in 1955.
Charles and other members of the royal family will be in Edinburgh this week to attend Holyrood Week – known as Royal Week – which takes place each summer.
Last week, Charles and Duchess Camilla were in Rwanda for the Commonwealth Heads of Government Meeting and delighted royal fans as their visit drew to a close.
Charles is set to spend time in Edinburgh this week
Taking to Instagram on Sunday, the pair delighted fans with glamorous snaps from a special dinner they hosted for the leaders of the Commonwealth.
One snap captured the stunning sapphire blue gown worn by the Duchess who was wearing her Garter Star alongside Prince Charles, who like his wife, donned the important badge.
One fan wrote: "The Duchess looked stunning last night. The Garter Star suits her perfectly," said one fan.
A second replied: "I’m really proud of Camilla, she seems to have stepped up to the role just right!!" A third added: "Camilla looks stunning in that cobalt blue gown. One of her best evening wear looks so far!"
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