The chief ombudsman’s departure was announced by Fos on 15 November and chairman Sir Nicholas Montagu said Ms Ceeney felt the time was right to “move on”.
A spokesman for Fos said Ms Ceeney would take annual leave that she had accrued and would assess what her next role should be, although her next move was not yet known.
She added that Ms Ceeney had been “worked quite hard” in recent years and would now take the opportunity to have a break away from the industry.
Deputy chief ombudsman Tony Boorman will take her place until a replacement is found.
Ms Ceeney, 42, had previously spoken about industry hostility and sexism on her appointment with Fos, with comments focused on her lack of financial experience or her appearance.
Ms Ceeney said: “I hate the box-ticking exercise and I would hate to be put in a position where I got the job because I was female, rather than being the best candidate.
“But why does talking about female representation matter? There is a lot of scientific evidence that the best teams have a mixed-gender representation. Importantly women account for half the population.
“Having senior management making the jobs inaccessible to half the population cannot be the best way to harness talent.”
Ian Thomas, director of Devon-based Pilot Financial Planning, said: “While Ms Ceeney came into Fos from outside the industry, it has been hiring people from the industry at a senior level who understand how the game works and one would hope that would continue in future.”
Ms Ceeney joined the Fos in March 2010. She was previously chief executive of The National Archives from 2005 to 2010.
Prior to that post she was director of operations and services for the British Library from 2001 and strategy consultant for McKinsey & Company from 1998.
A statement from Fos stated that it had trebled in size under Ms Ceeney’s stewardship and had just received its one millionth complaint on mis-sold payment protection insurance.