The protest took place under the banner "No to Boris. Yes to Europe," with the route passing Buckingham Palace and ending outside the Houses of Parliament.
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Demonstrators gathered in the city's Parliament Square, where organizers flew a giant balloon puppet of Johnson.
Conservative party leader resultBritain's ruling Conservative Party is set to announce the successful candidate on Tuesday.
Both Johnson and his rival Jeremy Hunt have said they will take Britain out of the EU with or without any withdrawal agreement.
Organizers said the aim was to "make it clear to Boris Johnson that [they] want to stop the Brexit chaos."
"This is a national emergency. We won't put up with a hard Brexit PM being imposed on the country and hurtling us towards the cliff edge," the organizers said.
Amid a string of speeches was a performance from singer-songwriter and left-wing activist Billy Bragg.
The effigy of Johnson included the politician's trademark disheveled hairstyle and a T-shirt featuring a bus and the message "£350m." The reference was to a claim made on the tour bus of Johnson's 2016 Vote Leave campaign. It said that Britain could save £350 million per week (€390 million, $440 million) and instead spend it on healthcare.
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Johnson later backtracked on the claim, which was described as "misleading" by Britain's Office for National Statistics.
"The Boris Blimp might seem a bit of lighthearted fun but it carries a serious message," said Tom Brufatto, one of the protest organizers.
Some 160,000 Conservative Party members will decide on the successor to Prime Minister Theresa May, with both candidates having promised that Britain will leave the EU on October 31.
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