Sir Keir is not thought to have any Covid symptoms but the infection was picked up as part of his regular testing routine.
The Labour leader previously tested positive for coronavirus on the day of the Budget in late October, before returning to work in early November.
His latest positive test will mean it is the sixth period of self-isolation for the Labour leader since the start of the pandemic.
On four occasions between September 2020 and July 2021 Sir Keir stayed at home after family members, staff or contacts tested positive.
The positive test comes a day after the Labour leader travelled to Birmingham for a major speech setting out his vision for Britain’s future.
On Tuesday, Sir Keir addressed an audience where he promised “straight leadership” based on the values of “security, prosperity and respect” if his party is returned to power.
The Labour leader also called for an expansion of testing in schools to avoid year groups being sent home and widespread closures. Sir Keir said Labour would back the self-isolation period being cut from seven to five days, so long as scientific advisers recommended it.
His own positive result comes as Covid testing rules are set to be eased to reduce the time people have to spend in isolation, with Mr Johnson under pressure to combat staff absences in key parts of the economy and health service.
People who test positive on a lateral flow test will no longer need a confirmatory PCR to begin the self-isolation period if they do not have symptoms, potentially allowing them to return to work earlier, under plans being considered by ministers.
The change could be announced on Wednesday as the prime minister argues to his cabinet they should stick by the plan B measures in England – despite admitting parts of the health service will feel “temporarily overwhelmed”.