Lucy Adams, the BBC's head of Human Resources, is to leave the corporation in March 2014 after five years.
Ms Adams, who is paid £320,000 a year, will leave at the end of the financial year without any severance pay.
She was heavily criticised by the Commons Public Accounts Committee in a hearing last month over excessive payments to departing BBC executives.
Tony Hall, the BBC's director general, said he would be "very sorry to see her go next spring".
In a statement, Ms Adams said it had been "a great privilege to lead the BBC's People division" and that she had been planning to leave "for some time".
"By next spring I will have been at the BBC for five years which feels like a good time to try something new.
"The BBC is a unique institution and I am extremely proud of the work the team has achieved in spite of the challenges along the way," she continued.
"I look forward to continuing that work with Tony and the executive board in the coming months."
Lucy Adams joined the BBC as the director of BBC People in June 2009 and is responsible for the design and implementation of the corporation's HR strategy.
Previously the director of HR at legal firm Eversheds, she also spent nine years with security firm Serco.
When asked in July why there had been overpayments to BBC executives, she said "the overwhelming focus was to get numbers out of the door as quickly as possible".
In a Daily Mail article published ahead of her appearance, she was described as one of "the [BBC] bosses in charge of the gravy train".
Lord Hall said Ms Adams had "done a great job and contributed a huge amount to the BBC".
"I am pleased that, in the short term at least, she will continue to help me simplify the way we do business in the BBC so that we can spend more time concentrating on our programmes and services."