Mr Johnson had been due to return from the US on a different plane but altered his plans at the last minute, giving the pair crucial time ahead of a meeting in which Ms May will brief ministers on her Brexit plans.
It follows reports that Mr Johnson was threatening to resign from the frontbench if Ms May softened her stance on EU withdrawal, which she will set out in more detail in a major speech in Florence on Friday.
The Foreign Secretary was all set to return separately from the United Nations General Assembly, but Ms May’s official spokesman confirmed he would join the Prime Minister on her RAF Voyager jet on Wednesday evening.
The flight will give them an opportunity to talk in more detail over Ms May’s plans for Brexit, which have now had to be carefully balanced to keep Mr Johnson and other Brexiteers happy, while also satisfying those wanting a more business-minded withdrawal, like Chancellor Philip Hammond and Home Secretary Amber Rudd.
Relations between Ms May and Mr Johnson have been strained since the Foreign Secretary wrote a 4,000-word article in The Telegraph setting out his vision for Brexit, despite Ms May having already announced that she was to give a key speech on the EU.
Reports that he would quit if Ms May committed the UK to permanently paying for access to the EU’s single market were denied, but caused enough concern for the two to hold talks in the US.
Ms May and Mr Johnson met on Tuesday night at a reception for Commonwealth leaders at the UN for the first time since the ex-London mayor had published his explosive personal Brexit manifesto.
The Prime Minister’s spokesman gave no details of any conversation that the pair had at the event.
But afterwards in New York during the trip, the Foreign Secretary said, “Of course not” when asked whether he was going to quit, and predicted the Government would “deliver a fantastic Brexit”.
Asked whether there was a Cabinet split on Europe, Mr Johnson said: “No, we are a government working together. We are a nest of singing birds.”
The Foreign Secretary had said on Monday that his article was meant to be an “opening drum roll” for the PM’s speech, adding: “Because I was involved in that Brexit campaign, people want to know where we are going.”
But that did not stop many key figures in his own party accusing him of disloyalty to the Prime Minister, and attempting to set out his own leadership credentials as she prepared to give her speech in Florence.
EU leaders are expecting Ms May to offer €20bn (£17.7bn) for the so-called Brexit divorce bill, according to reports, with the figure only covering short-term obligations until 2019, and has been described as a “transition payment”.
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