The Labour leader was said to have tested negative in the morning ahead of his appearance in Parliament where he grilled Boris Johnson over his isolation policy.
It is the fourth time Sir Keir has had to enter quarantine since the pandemic began and will force him to alter plans to launch his "safer communities" campaign on Thursday.
A spokesman for Sir Keir said: "One of Keir's children tested positive for Covid this lunchtime. In line with the rules, Keir and his family will now be self-isolating.
"Keir was already doing daily tests and tested negative this morning. He will continue to take daily tests."
The news came shortly after the Labour leader appeared at Prime Minister’s Questions with Mr Johnson - who is also self-isolating after the NHS notified him that he had been in contact with someone who tested positive for Covid-19.
At a chaotic final session before summer recess, Sir Keir branded Mr Johnson a "super-spreader" of confusion and warned the country faces a "summer of chaos" as he highlighted policy changes over isolation exemptions for people pinged by the NHS app and vaccine passports for nightclubs.
He added Mr Johnson's new three-word slogan should be "get a grip", amid reports it will be "keep life moving".
But the Prime Minister, dubbed the "Chequers one" by Sir Keir due to his appearance virtually from isolation at the country retreat, described the Opposition leader's questions as "feeble stuff" and defended his decisions during the pandemic.
Sir Keir's statement announcing that he will swiftly enter quarantine with his family will doubtless be contrasted with the Prime Minister's own approach over the weekend.
Mr Johnson and Chancellor Rishi Sunak initially tried to get around quarantine after being contacted by NHS Test and Trace by saying they would join a daily workplace testing programme.
But they were forced to back down on the plans and enter isolation amid widespread public anger that they would be free while tens of thousands of people are forced to miss work or school over coronavirus contacts.
Addressing the television screen in the Commons chamber on Wednesday, Sir Keir accused Mr Johnson of having tried to "dodge" quarantine.
The Labour leader had been due to head to Wolverhampton on Thursday as part of a drive to win back support from voters.