Confirmation of her departure came as her deputy was announced as her replacement, on an interim basis.
Kate Bingham was appointed as chairman of the government’s vaccine task force in May.
Since then she has won praise from ministers for securing millions of doses of the three vaccines, so far, which scientists have found to be effective against Covid-19.
But she faced criticism when it was reported that Ms Bingham, a former venture capitalist and the wife of Jesse Norman, a Tory minister, had used the services of eight consultants to advise her on media strategy.
Last month reports suggested that Ms Bingham’s contract was due to run out at the end of the year and that she had always intended to leave at that point.
As her replacement was announced, Boris Johnson said he was “hugely grateful for the hard work and dedication of the vaccine task force, under Kate Bingham’s leadership … the country owes them a debt of gratitude.”
In response Ms Bingham thanked the prime minister, saying the clear mandate he had given the taskforce had allowed them to strike deals for promising vaccines.
Clive Dix, currently the deputy chair of the taskforce, will step into her role.
He warned that although the UK now had vaccines against the virus there was “more for us to do.
“We must continue to develop our research and response capabilities in the UK and finish the task of building an infrastructure to enable us to manufacture vaccines at scale.”