The Treasury acted on advice from the FCA board.
A permanent FCA CEO appointment is expected in due course and a search is under way.
Mr Woolard is currently the FCA’s executive director of strategy and competition and a member of the FCA’s board.
He is responsible for the FCA’s policy output, its work on innovation, competition and economics and for helping direct the strategy for the financial regulator.
He joined the Financial Services Authority (the FCA’s predecessor) in 2013 and helped lead the creation of the FCA. Before that, he worked at Ofcom (2009-2012), the BBC (2005-2009) and in the civil service (1995-2005).
Mr Woolard, said: “I’m delighted that I’ve been asked to take on this role. We have a huge job to do and I’m looking forward to working with the board and colleagues across the FCA as we continue to deliver the FCA’s mission.”
FCA chairman Charles Randell said: “I’m looking forward to working with Chris in his interim chief executive role. I’m confident that he and executive committee colleagues will continue to deliver our ambitious plans for change in 2020 and beyond, building on the foundations laid by Andrew Bailey.”