Hector Sants is to quit the FSA in the summer, and will not become deputy governor of the Bank of England or CEO of the Prudential Regulation Authority.
In a statement, the outgoing CEO said said: "When I agreed to stay on as CEO in 2010, I committed to stay and deliver an orderly transition to the Government's new regulatory structure.
"The project is now firmly on track and with the establishment of twin peaks within the FSA I will have achieved that goal.
"Now is the right time to hand over to those who will deliver the long term goals of the future PRA and FCA.
"I am proud of what the FSA has achieved during my time in charge, through what have been incredibly challenging times. I would like to thank all of my colleagues for their dedication, support and hard work. I know I leave the organisation in very capable hands."
In February 2010, Sants announced his resignation and was due to step down as CEO of the FSA in the summer of 2010, after three years in the position.
However, in June 2010 the new Government announced its plans to change the UK's financial regulatory framework from an integrated model to a "twin peaks" model, with prudential and conduct supervision to be carried out by two new organisations - the Financial Conduct Authority (FCA) and the PRA.
Sants's last day will be the 29th June. Andrew Bailey will take over Hector's role as head of the Prudential Business Unit (PBU) the part of the FSA mirroring the future PRA, Martin Wheatley will remain the head of Conduct Business Unit (CBU) and future CEO of the FCA. Following Hector's departure both will directly report to Lord Turner.
Sants was appointed FSA Chief Executive in July 2007. He joined the FSA from Credit Suisse in May 2004 as managing director of the wholesale and institutional markets at the FSA.
In January, Sants claimed he had never intended to become the chief executive of the regulator and had to be "talked into" apply for the role.
‘Important to have an anchor’
Lack of innovation for solutions
Some 2,000 consumers affected
Achievements, charity work and other happy snippets