Flybe said it has kicked off the process of finding a successor.
De Klerk has been with Flybe since August 2014. He was previously global head of financial planning and analysis at SABMiller plc (LON:SAB) and spent 16 years at Unilever plc (LON:ULVR) in a variety of finance roles.
Last month in a trading statement ahead of its full year results in June, Flybe said revenue had been hit by weak demand, tough pricing competition, poor weather and strikes by French air traffic controllers.
Issues with software and IT contracts were also expected to take up to £10mln off profits as it conducts an overhaul of its systems to improve its online offering.
Flybe cut costs and reduced capacity to respond to the challenges. It saw seat capacity growth fall by 10% in the final quarter of 2016 after a 12.7% decline the previous three months.
Shares in the airline were little changed at 39.75p while shares in Low & Bonar dropped 1.24% to 79.50p in morning trading.