Mr Johnson was making a speech at the "convention of the north" in Rotherham when he was interrupted by the heckler.
The male screamed: "Maybe get back to Parliament. Yeah? Why are you not with them [MPs] in Parliament sorting out the mess you created?"
As the heckler continued to shout, the Prime Minister replied, with a smile: "I am very happy to get back to Parliament soon, but what we want, I think, to see in this region is towns and communities able to represent that gentleman and sort out his needs."
The man was then forcefully ejected from the room by security guards.
After being heckled, Mr Johnson insisted there would be "ample time" for MPs to debate any Brexit deal ahead of the October 31 deadline. Parliament returns on October 14.
It came hours after Mr Johnson was told he had “a cheek” to visit Doncaster during a visit to the town's busy marketplace.
An angry voter confronted the Prime Minister for telling the public a “fairy tale” over Brexit.
Boris Johnson promises October 31 Brexit date on trip to Doncaster market
In the exchange captured on video, a woman told Mr Johnson: “People have died because of austerity.
“And you’ve got the cheek to come here and tell us austerity is over, and it’s all good now, and we’re going to leave the EU now and everything’s going to be great. It’s a fairytale.”
Last week in Morley - Boris Johnson was told #PleaseLeaveMyTown.
Today - it’s Doncaster.
“People have died because of austerity. And you’ve got the cheek to come here.”#NorthernStrategy pic.twitter.com/J4qmKIAoMN— Clare Fallon (@clarefallon)September 13, 2019
Mr Johnson started to respond by saying “well actually we have a lot of” but was then interrupted by a crowd shouting as they gathered around the pair.
During his trip to the market, the Prime Minister had told one trader "we're going to get a deal", adding: "That's the plan, anyway. And if we don't, we're coming out on October 31. That's what we're going to do. Here we go, that's democracy."
Mr Johnson was surrounded by excited shoppers as he visited the sunny south Yorkshire town, which voted by 69 per cent to leave in the EU referendum but has been regarded as a Labour stronghold in past elections.
He showed no reaction as one man told him: "Find a deal here - this is Doncaster, not Europe."
As he walked around stalls inside the market's indoor Corn Exchange, the Prime Minister stopped to speak with one fish seller.
With Northern Powerhouse minister Jake Berry watching on, Mr Johnson was heard remarking: "Look at that... lobster claws. We've got to take a few claws out of that Withdrawal Agreement."
After stepping outside into the packed marketplace on Friday morning, Mr Johnson reassured one shopper: "We'll get you out, we'll get us out."
As he visited a fruit stall, the Prime Minister moved towards some Belgium strawberries, before eventually buying English Victoria plums.
The Prime Minister was visiting south Yorkshire after northern politicians made a joint call for more help in their regions from his government.
In a joint article in The Times, Greater Manchester mayor Andy Burnham and Liverpool city region mayor Steve Rotheram said: "To get this country working again, there is an urgent need to take power out of Westminster and give it to our great cities and regions.
"We need to build a new, healthier politics that unifies people around place and positive change and delivers practical change for citizens."
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They identified five "priority areas" for the government, including the termination of the Northern Rail franchise with more local control of rail services, London-style subsidies for northern bus services, central funding to help people affected by clean air zones to switch vehicles, action on homelessness and more devolved powers putting more money under their control.
The two mayors both also support two major projects to improve transport in the regions, HS2 and Northern Powerhouse Rail, but called for more money and powers to be devolved from Whitehall to the regions.