Both sides say the leaders need to “take stock” of trade negotiations, as the deadline for a deal looms.
Boris Johnson will hold talks with the head of the EU Commission – a day after she began legal action over his plan to potentially override the Brexit deal.
Ursula von der Leyen and the prime minister are due to talk on Saturday afternoon.
A Number 10 spokesperson said it is to “take stock of negotiations and discuss next steps”.
Brussels confirmed the news and added the conversation will be taking place over a video call.
While the two leaders will likely be focusing on trade talks to hammer out an agreement before the transition period runs out at the end of 2020, Ms von der Leyen’s action yesterday will inevitably feature.
She accused Mr Johnson of breaching the “good faith” part of the withdrawal agreement, by drawing up a plan to override it in the event trade talks are unsuccessful.
A minister has admitted the move would break international law.
Before Mr Johnson and Ms von der Leyen’s call, the UK and EU’s two chief trade negotiators – Lord David Frost and Michel Barnier – will meet today.
Both sides need to agree a deal by a 15 October deadline – the next meeting of all EU leaders where they would gather to sign it off.
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Sources told Reuters that so far talks have “failed to resolve all the outstanding issues”.
The main stumbling blocks remain the issues of future fishing rights and state aid rules.
Mr Johnson has said previously he is prepared for there to be no deal.
‘Time for those at the top to put their cards on the table’
Analysis by Michelle Clifford, Europe correspondent
Wouldn’t you like to eavesdrop on that Saturday morning conversation between the man and woman either side of the Channel trying to deliver a Brexit deal with so little time left.
That they are talking at all has to be seen as a positive.
The call between the two will come just two days after the EU launched legal proceedings against the UK over its plans to override parts of the withdrawal agreement.
One imagines there will be some time set aside for some firm words about that but the aim of the call is for the two to “take stock” of this week’s negotiations and figure out the next steps with just weeks left now until a deal is supposed to be decided.
The EU has remained tight-lipped about talk of some progress from the UK side but has acknowledged there are still significant gaps between their positions.
Will a frank conversation between the two shove things in the right direction?
Negotiation teams have been hard at it in Brussels all week. The EU and UK chief negotiators met today.
But it’s now time for those at the top of the talks to put their cards well and truly on the table.