He "isn’t formally doing government work" but he and Mr Trump "agreed on the importance of a co-ordinated international response to coronavirus".
“They also discussed continued UK-US co-operation in the fight against the pandemic," a spokesman added.
Mr Johnson will resume his weekly audiences with the Queen when he speaks with her on the phone later this week.
The prime minister's spokesperson said it will be the first time in three weeks that Mr Johnson has spoken to Her Majesty - who is celebrating her 94th birthday.
The PM has been receiving updates from Number 10 and ahead of PMQs spoke with his deputy, First Secretary Dominic Raab, who will face questions in his place as the Commons goes virtual for the first time ever.
Mr Raab will face new Labour leader Sir Keir Starmer, who will be levelling questions in a virtual format.
Mr Johnson is expected to thank Mr Trump for the messages of support he sent while he was unwell with coronavirus, spending several days in intensive care.
The PM will also receive an update on the international G7 response to Covid-19 - the US is the current G7 president.
Mr Johnson’s spokesperson added: “Later this week, the Prime Minister is expected to have an audience with Her Majesty the Queen and that will be the first for, I believe, three weeks.”
Downing Street also said Foreign Secretary Raab will chair a meeting of the Cabinet on Thursday morning.