Ceeney joined the FOS in March 2010, with various senior roles under her belt but no previous experience in financial services.
Following her departure the FOS will be run by deputy chief ombudsman, Tony Boorman, until further notice, it said.
FOS chairman Sir Nicholas Montagu, who made the announcement, said: “In the close to four years since joining, Natalie (pictured) has taken the service from dealing with an annual workload of 150,000 cases to over 500,000 cases – with the organisation trebling in size under her leadership in response to the challenges of PPI.
“So having just received our millionth new PPI complaint, Natalie feels that now is the time for her to move on – as the ombudsman service itself starts out on a new set of challenges, building on the foundations for change laid under Natalie’s leadership.
“The board and I are very grateful to Natalie for her achievements as head of the ombudsman service – which under her leadership became a Sunday Times ‘top 100’ best employer, resolving up to 2,000 consumer disputes a day.”