Scott, who is currently director of financial reporting, will assume his new role on January 1, with Healy standing down on March 31.
Healy joined Thomas Cook in May 2012 and over the last five years has led a restructure of Cook’s finances to support the transformation of the business.
Following his retirement, Healy will continue to oversee two of the key areas of future growth for the group as deputy chairman of Thomas Cook China and chairman of Thomas Cook Money.
Frank Meysman, chairman of Thomas Cook, said: “Michael will leave Thomas Cook a much stronger and more resilient business than the one he joined five years ago.
"I would like to thank Michael for the very significant contribution he has made to the financial health of the group and I am pleased that he has agreed to continue his involvement in the business through non-executive leadership roles in Thomas Cook China and Thomas Cook Money, both exciting areas of growth."
Elsewhere, Scott has previously held senior financial positions across a range of businesses in the UK and Asia, including Kwik Fit, PricewaterhouseCoopers, First Pacific Company and Shell.
Meysman added: “I look forward to welcoming Bill to the board in the new year to support us through the next phase of the group’s development.”