Mr Johnson met with a group of MPs on Thursday for 35 minutes, including Ashfield MP Lee Anderson, who has subsequently tested positive for Covid-19.
A spokesperson for the PM said: "The prime minister has today been notified by NHS Test and Trace that he is required to self-isolate as a contact of someone who has tested positive for Covid-19.
"The Prime Minister will follow the rules and is self-isolating.
"He will carry on working from Downing Street, including on leading the government’s response to the coronavirus pandemic.
"The PM is well and does not have any symptoms of Covid-19."
Mr Johnson tweeted he has no symptoms and will "continue to lead the government's pandemic response", late on Sunday night.
Mr Johnson tested positive for Covid-19 at the end of March and was admitted to a London NHS hospital on April 5, which Downing Street said was a "precautionary step" as his symptoms persisted.
He then spent three nights in St Thomas' Hospital's intensive care unit, later revealing it "could have gone either way" and thanked NHS staff for saving his life.
It is not yet known, but thought possible, that people can catch the respiratory disease twice.
Political Correspondent Paul Brand reported that Downing Street are looking into how the PM can still participate in Cabinet on Tuesday and also other parliamentary business.
He adds it is unlikely Mr Johnson will be able to take part in PMQs on Wednesday.
Paul Brand adds that Mr Johnson was hoping to make a break with the recent few days which have been overshadowed by the departure of his chief aides Dominic Cummings and Lee Cain, but instead "he'll be holed up inside Number 10 unable to get out there on the front foot".
However, a spokesperson said the prime minister will continue working from Number 10 and is expected to lead a Downing Street press conference this week.
In a post on his official Facebook page, Mr Anderson wrote both he and his wife had tested positive for coronavirus and while they both feel "good" he is concerned about his wife who is shielding.
"On Friday I lost my sense of taste at the same time my wife had a bad headache," Mr Anderson wrote.
"I had no cough, no fever and felt well.
"We both had a test on Saturday and the result came in Sunday morning.
"My wife and I both tested positive.
"I feel absolutely fine and my biggest concern is my wife who is in the shielded group.But we are both feeling good."
On Thursday, Mr Anderson posted a picture of himself with the prime minister after the breakfast meeting in Downing Street - both not wearing face coverings and appearing to be less than two metres apart.
Downing Street insisted that Number 10 is a Covid-secure workplace and every step is taken to minimise infection, but due to the length of the meeting Mr Johnson was advised to self-isolate.
On Monday, the Prime Minister was expected to meet Tory MPs from the newly formed Northern Research Group (NRG), which was set up to press the case for "levelling up" northern England.