According to Dominic Cummings, Johnson's controversial former special adviser, the PM was shocked when he began to understand the implications of leaving the trading bloc - despite working on the Vote Leave campaign in 2016 and winning the 2019 election on the slogan "Get Brexit Done".
Cummings wrote in his blog: "I will never forget the look on his face when, after listening to Frost in a meeting** on the final stage of negotiation, he said, 'No no no Frosty, f**k this, what happens with a deal?"
According to Cummings, Lord David Frost, cabinet minister and then chief negotiator of Taskforce Europe, responded that this what leaving the Customs Union looked like - to the prime minister's surprise.
"The PM's face was priceless," Cummings continues.
"He sat back in his chair and look around the room with appalled disbelief and shook his head."
Cummings adds that he then got a text from "one very senior official" who said "Now I realise how you managed to get Brexit done" accompanied with a crying with laughter emoji.
The former special adviser finishes the section of his blog with: "As Hunter S Thompson said, humour in politics is usually dark."
Membership of the customs union was a critical part of the Brexit negotiations. Being a part of it would have allowed an easier flow of goods, but would not itself guarantee frictionless trade and would limit - though not prevent - Britain’s capacity to strike its own free trade deals.
In 2016 while foreign secretary in the aftermath of the referendum, Johnson claimed that "we will probably have to leave the customs union" but added: "I believe it can be done and at the same time maintain free trade".
This ascertain was rejected by German chancellor Angela Merkel, who said at the time that the EU could not separate the four freedoms to allow Britain to restrict immigration from the bloc while retaining tariff-free access to the single market.
Since Cummings' dramatic exit from Number 10, he has made it clear he has an axe to grind with the prime minister, saying: "The sooner he goes the better, for sure".
They became estranged last year following power struggles within Downing Street and Cummings' apparent unhappiness with Johnson's management of the pandemic.
Following his resignation, he appeared before parliament's health and social care committee where he described what he portrayed as chaotic scenes and incompetence at the heart of government at the beginning of the pandemic - even expressing guilt about the role he played in the response.
He regularly posts detailed, inside information about the goings-on at the heart of government on social media and his blog from his time in Downing Street - including screenshots of conversations he had with the prime minister at the beginning of the pandemic.
“I must say I have been slightly rocked by some of the data on Covid fatalities," the prime minister appears to write on WhatsApp to Cummings in October 2020.
"The median age is 82 to 81 for men 85 for women. That is above life expectancy.
"So get COVID and live longer."
Cummings has also previously said he discovered his "hopeless" traits after working with him during the 2016 Brexit referendum - but supported him against former Labour leader Jeremy Corbyn as he believed he was the better option.
Cummings became a household name last year after it emerged he had made multiple trips to Durham during the first lockdown despite having tested positive for COVID-19.
Number 10 staunchly defended Cummings, but public outrage was so severe that he was forced to hold a special press conference in the Downing Street garden.
Yahoo News UK has contacted No 10 for comment.
Watch: Dominic Cummings calls Boris Johnson a ‘joke’ following MP report into Covid errors