Cole will remain in her current role on the FSA board until the end of March prior to the creation of the twin peaks within the FSA on 2 April.
She will then be on gardening leave until 31 August 2012 but may represent the FSA during that time on issues not related to individual regulated firms or ongoing investigations.
Cole joined the FSA as director of enforcement in July 2005 following 20 years in private practice specialising in commercial litigation.
Cole said: “I joined the FSA to help in the fight against wrongdoing within the financial services industry and I believe a lot has been achieved in my time here.
“We have shown the FSA is not afraid to take on difficult cases and will not shy away from pursuing criminal prosecutions, however difficult to prove.”
Managing a division of 450 people, Cole had responsibility for enforcement policy, intelligence gathering, forensic investigations and civil and criminal proceedings in areas that include market abuse and financial crime.
She added: “It’s painstaking work and the legal process takes a long time but there are people sitting in prison now because of our commitment. The next 12 months will see more trials and more convictions as the pipeline of our cases comes to fruition in the courts.”
Cole led the FSA’s drive to deliver its credible deterrence strategy which in 2011 saw 11 convictions for insider dealing with sixteen awaiting trial and fines levied totalling £66m.
She was appointed to the FSA Board as managing director of enforcement and financial crime in September 2010 and in April 2011 took on the role as the first managing director of the conduct business unit which will go on to become the Financial Conduct Authority under the new regulatory structure.
In that role she led the work that established the architecture and delivered the blueprint for the future FCA’s approach and has played a frontline role the FSA’s involvement in the current regulatory reform legislation.
Cole concluded: “It has been a challenging but rewarding few years and I believe, with the help of a team of quality people, I have created a successful enforcement platform to take into the UK’s new regulatory authorities.
“The time has come for me to seek a fresh challenge, knowing that I leave the continuation of a winning strategy in safe hands.”
Hector Sants, chief executive of the FSA, said: “Margaret has been pivotal in transforming the FSA’s approach to enforcement and she leaves a substantial legacy, widely respected in legal, regulatory and international circles.
“She has been a strong leader and advocate of the importance of delivering a credible deterrent to those that attempt to commit wrongdoing, as well as being an invaluable member of my executive team.
“Her expertise across a broad range of management disciplines and the work she has done in setting up the conduct business unit has put us in good shape to develop the future conduct regulator.
“I would like to express my personal thanks and those of the organisation, for all that Margaret has achieved and I wish her every success in whatever future challenge she chooses next.”
Adair Turner, chairman of the FSA, said: “On behalf of the FSA board, I would like to extend my appreciation to Margaret for her outstanding contribution to the effectiveness of the FSA over the years, her strong management credentials and for the expertise and quality judgement she has brought to our board discussions.
“She has made a lasting impact. We will be sorry to lose her for the organisation’s final year but she will depart with our thanks and best wishes.”
Martin Wheatley, chief executive officer-designate of the FCA, said: “I’m enormously grateful to Margaret for establishing the conduct business unit, which will go on to form the foundation of the Financial Conduct Authority.”