Sarah Sands is standing down as editor of BBC Radio 4s Today programme after three years.
The news comes a day after it was announced that 450 jobs are to be cut from BBC News under plans to complete its £80m savings target by 2022.
Sands, who took over the reins of the flagship news show in 2017, said it was "a good time to move on".
She previously edited the Evening Standard, where she was replaced by former chancellor George Osborne.
BBC News announces 450 job cuts
"I have decided that September is a good time to move on from editing the Today programme," she said in a statement.
"I have loved being part of the Radio 4 team and am proud of what we have achieved, championing intelligent broadcasting and political independence."
She added: "The Today programme is a beacon of news journalism and I wish it and the BBC well."
Other outlets to be hit by the job closures announced on Wednesday include BBC Twos Newsnight, BBC Radio 5 Live and the World Update programme on the World Service.
Speaking outside the BBC on Thursday morning, Today presenter Nick Robinson said he was "incredibly sorry" to see Sands go, noting that "shes made a big impact on the programme".
Fran Unsworth, the BBCs director of news, said in a statement: "Sarah has brought new ideas and fresh thinking to the Today programme over the past three years.
"Under her editorship she has broadened the programmes agenda, putting a renewed focus on science and arts, and left the nation scratching their heads with the puzzle for Today."
She went on: "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."
Sands made changes to Radio 4s flagship programme, including fashion coverage and the introduction of Puzzle for Today, a "humiliatingly hard" morning quiz.
Writing in the i newspaper at the time, she said: "The puzzle speaks to the ingenuity of this country. We have a history of problem solving."
Under her tenure, Sands also had to deal with the fallout from the publication of the BBCs star salaries, which revealed that Today and Mastermind presenter John Humphrys earned between £600,000-£649,000 in 2016/17, while his Today co-host Sarah Montague received less than £150,000.
Humphrys took a pay cut and has since left the programme, while Montague has won back pay of £400,000 in an equal pay settlement.
As she made clear in her email to staff, Sarah Sands was never going to be a lifer at the BBC.
As editor of a paper like the London Evening Standard, she had huge autonomy and commercial obligations. Editing Today, there are fewer commercial obligations, but editorial freedom is more conditional. You couldnt drop Thought for the Day, for instance, without getting sign-off from higher authorities.
Moreover, its a sad truth that running one of the BBCs most high-profile shows comes with a daily dose of abuse and tedious conspiracies on social media.
Of course, its impossible to separate Sands departure from the wider travails of BBC News. A major reorganisation risks weakening programme editors. Big savings need to be made, including at Today. John Humphrys left recently.
And ministers are - for now - boycotting the programme. Thats despite the fact that Sands knows the prime minister very well. Not only were they on the Telegraph together years ago, but Sands ran Londons paper when Johnson was the citys mayor.
Running any BBC show these days is tougher than it used to be. Abuse on social media, declining linear audiences, and smaller budgets hurt. But it is the political profile of Today that will make her successors job so tough.