She will leave the position at the end of February but will stay with the FSCS as special adviser to the board until the end of August.
The FSCS is yet to name a replacement.
Minghella has been chief executive since December 2004. Previous to this, she was the FSA’s first head of enforcement law, policy and international co-operation.
Chairman David Hall says: “Loretta has steered the organisation skilfully through extraordinary times, overseeing the delivery of over £21bn of compensation in a number of innovative ways.
“She has also made an important personal contribution to improving the UK’s banking resolution and compensation system through her work with HM Treasury, the Bank of England and the FSA on legal reform.
“I am sure Loretta will be highly successful in whatever she decides to do next. She will leave with our very best wishes for the future.”
Minghella says: “It has been a great privilege to lead the FSCS over the past five years and it will be hard to say goodbye to so many excellent colleagues but I believe that it is time for me to move on to a new challenge.
“The organisation is only eight years old and yet it has already achieved an enormous amount, compensating over three million consumers and playing an increasingly important role in supporting financial stability. This record of delivery has provided a platform on which the FSCS is now building an even stronger organisation for the future.”