Sarah Sands has quit as editor of the Today programme, as the BBC announces a swathe of cuts in news programmes.
The broadcaster must now find a new editor for the flagship Radio 4 show before Sands leaves in the summer.
The editor denied speculation about her departure before Christmas.
On Thursday morning she emailed staff to say she was moving on after three years in the top role.
Her departure comes as the BBC plans to focus on digital news and concentrate its efforts on fewer stories.
Sands, who is leaving as the BBC prepares to appoint a new director general and faces threats over the licence fee, tweeted: “God bless the BBC.”
She wrote: “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.”
The long-running programme, presented by Justin Webb, Mishal Husain, Martha Kearney and Nick Robinson, was once guaranteed to be a big draw for politicians.
But the likes of Boris Johnson and Jeremy Corbyn have stayed away from the early-morning show, which has also focused on science and arts in recent years.
Its veteran journalist John Humphrys left last year, after 32 years and 5,000 programmes.
In October, Today recorded its lowest number of listeners in a decade, drawing an average weekly listenership of 6.60 million in the third quarter of 2019.
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.
Sands, the former editor of the Evening Standard, was the second woman to edit the current affairs programme.
Radio 4 controller Mohit Bakaya said: “Sarah has held the reins at Today during a time of extraordinary politics, as well as intense scrutiny and challenge.
“She has done so with great poise and dedication, seeking to broaden the programme’s remit along the way, and I wish her luck for what she does next.”
BBC director of news Fran Unsworth said: “Sarah has brought new ideas and fresh thinking to the Today programme over the past three years.
“Under her editorship she has broadened the programme’s agenda, putting a renewed focus on science and arts, and left the nation scratching their heads with the puzzle for Today.
“She has commissioned a series of formidable guest editors from Greta Thunberg to the Duke of Sussex.
“We thank her for all her hard work and wish her well for the future after she leaves the programme this summer.”