An entry in Wednesday’s Court Circular, the official record of royal engagements, said: “The Rt Hon Boris Johnson MP (Prime Minister and First Lord of the Treasury) had an audience of The Queen via telephone this evening.”
It is the first time the two national figures have conducted their traditional catch-up chat in three weeks.
There are no details in the Court Circular of Mr Johnson having an audience with the Queen last week when she was advised to rest and cancelled a two-day trip to Northern Ireland.
The Prime Minister was on holiday the preceding week, and the last official note of a telephone meeting between the pair was on October 6.
The 95-year-old monarch was due to travel to Scotland for the high-profile Cop26 evening engagement on Monday, but she will now record a video address for delegates.
It is understood the Queen very much wants the conference to be a success and result in meaningful action from the participating nations.
The Queen faced preliminary tests in hospital on October 20 during her first overnight stay at a medical facility in eight years, and has twice used a walking stick in recent weeks.
She returned to work on Tuesday, carrying out virtual audiences from Windsor Castle, her first official engagements in seven days, after she was ordered to rest by doctors – and later that day spoke with Chancellor Rishi Sunak ahead of the Budget.