He will be replaced on an interim basis by his deputy Sam Weihagen. The company adds that the search for a successor is underway and an “announcement will be made in due course”.
The news comes as the company announced operating profit fell to £20.1m in the three months to 30 June, down from £25.8m a year earlier.
Thomas Cook forecast the slump last month, its third profit warning in less than 12 months.
The company blames the poor performance on the continued unrest in the key Middle Eastern and North Africa destinations of Egypt, Tunisia and Morocco and difficult trading conditions in the UK.
It has launched a strategic review of its under performing UK business to look at the company’s current business model, prevailing consumer trends and how brands such as Cook and Going Places are positioned.
The company is set to form a joint venture with the Co-operative after Competition Commission gave the go-ahead for the two to create a company with 1,240 travel agents.
Fontenla-Novoa has been chief executive since 2003. He first joined Thomas Cook in 1972, working initially in its printing room before leaving in 1988 for International Leisure Group. He left to co-find Sunworld before rejoining Thomas Cook in 1996.