Mills was previously senior director or mergers and state aid at the Competition and Markets Authority.
In his new role, he will help deliver one of the FCA’s key objectives – to promote competition in consumers’ interest.
As well as responsibility for the watchdog’s sector market studies, he will deliver actions on anti-competitive behaviour in the financial services industry.
Mills will begin the role in November.
He said: “I am delighted to be joining the FCA to lead their expert and committed competition team.
“Financial markets face major change and complexity, so the FCA’s competition work is essential.
“I am looking forward to leading a programme of work which delivers real and lasting change for people and communities across the UK.”
Christopher Woolard, executive director of strategy and competition, added: “In Sheldon we are getting an undisputed expert in competition law and policy.
“I know that Sheldon will continue the ground-breaking and vital work the FCA has done since it was given a competition remit, to deliver markets that deliver for consumers.”