The 71-year-old has tested positive for COVID-19 and is displaying mild symptoms, Clarence House has said.
It said Charles "remains in good health" as he self isolates at home in Birkhall, Scotland.
The Duchess of Cornwall, 72, has also been tested but does not have the virus.
Buckingham Palace said Her Majesty the Queen remains in good health after last meeting the Prince of Wales two weeks ago on March 12.
In a statement, Clarence House said: "The Prince of Wales has tested positive for Coronavirus. He has been displaying mild symptoms but otherwise remains in good health and has been working from home throughout the last few days as usual.
"In accordance with Government and medical advice, the Prince and the Duchess are now self-isolating at home in Scotland.
"The tests were carried out by the NHS in Aberdeenshire where they met the criteria required for testing.
"It is not possible to ascertain from whom the Prince caught the virus owing to the high number of engagements he carried out in his public role during recent weeks.
"The Queen last saw The Prince of Wales briefly after the investiture on the morning of March 12 and is following all the appropriate advice with regard to her welfare."
But contact tracing is being carried out after the Prince held a number of private meetings with Highgrove and Duchy individuals, all of whom have been made aware.
A source said his doctor's most conservative estimate was that the prince was contagious on March 13, 24 hours after his last meeting with the Queen.
A small number of people living and working at Birkhall are remaining at the residence and self-isolating.