BThe heatwave of 2018, England's hottest summer since its inception, hit the company hard, prompting many potential clients to holiday domestically and not abroad.
Brexit fears and the loss in value of the pound have not helped, while it has also been struggling to compete with online operators.
Mr. Fankhauser faced one of his biggest challenges in 2015, as he strongly criticized how Thomas Cook had dealt with the deaths of two children on holiday in Corfu.
He admitted that the company had "shown no sympathy" after calling for the boycott of the company because of its behavior, which the parents of Bobby and Christi Shepherd, who died in 2006, described as "appalling".
A panel of investigators concluded that the operator had violated his due diligence after the children had died of carbon monoxide poisoning from a defective boiler.
"It's clear that there are things we could have done better as a company in the last nine years," said Fanhauser.
"In particular, the way we have led our relationship with the family, we will change.