The royals' three-minute journey, made to mark the London Underground's 150th anniversary, began in Farringdon and ended at King's Cross.
It had been 27 years since Prince Charles last went on the London Underground, when he opened Heathrow's Terminal 4. However, he and his wife were given specially-designed Oyster cards with £10 in credit to hop onto the underground carriage.
As part of their first joint trip on the Tube, the couple enjoyed posing for pictures by 'Platform 9¾' at King's Cross, where Harry Potter and his wizard friends would catch the train to Hogwarts in JK Rowling's popular Harry Potter series.
Prince Charles and Camilla were also shown a model of the King's Cross redevelopment project as well as the Crossrail development site at Farringdon station.
The Crossrail project, expected to open its central section in 2018, will run trains from Maidenhead in Berkshire to Shenfield in Essex.