Sarah Sands is standing down as editor of the Today programme after three years.
Her decision comes as the BBC announces a swathe of cuts in its news programmes.
A source has confirmed that Sands, the second woman to edit the current affairs programme, will be leaving the flagship BBC Radio 4 show.
Sands, the former editor of the Evening Standard, was appointed in January 2017.
The programme’s veteran journalist John Humphrys left last year, after 32 years and 5,000 programmes.
Top politicians were once guaranteed to go on the programme, but the likes of Boris Johnson and Jeremy Corbyn have stayed away.
It was recently revealed that former Today programme presenter Sarah Montague won a £400,000 settlement and an apology from the BBC after being treated “unequally” by the BBC for many years.
She said the deal came after a “long period of stressful negotiations” which was triggered after discovering a disparity in her pay and conditions.
BBC director-general Lord Tony Hall has said broadcasters have to be careful about contributing to a toxic discourse with political journalism aimed at trying to “catch out” politicians.
The programme is presented by Justin Webb, Mishal Husain, Martha Kearney and Nick Robinson.
Sands later confirmed she was leaving, tweeting: “I have decided to move on from being editor of the Today programme and propose to leave the BBC in September.
“It has been a privilege to be part of this remarkable team and I am proud to have championed our intelligent journalism and political independence. God bless the BBC.”