The Prime Minister, who only took office this week, was driven from Downing Street to meet Charles following his return to London from Balmoral.
Wearing a plain black dress, she was welcomed by the King who shook her hand at the first of what will be their regular weekly encounters.
Their discussions are private and by tradition details are never made public.
Earlier, Ms Truss led tributes in the House of Commons to the Queen as she urged the country to support their new monarch.
She told MPs the King “bears an awesome responsibility that he now carries for all of us”, adding: “Even as he mourns, his sense of duty and service is clear.”
She said the British people, the Commonwealth and all MPs must support Charles as he takes the country forward to a “new era of hope and progress, our new Carolean age”.
While “our lives changed forever” with the death of the Queen, she said Britons must show the world “we do not fear what lies ahead”.
On Tuesday, Ms Truss met the Queen at her Scottish estate when she was invited to form a Government following her victory in the Conservative leadership contest.
On Saturday, she will attend the Accession Council in the State Apartments of St James’s Palace where Charles will be formally proclaimed King.