He achieved 77.1% of the maximum bonus available based on a number of criteria, including the group's profit, cash flow and its 'customer at heart' strategy.
His total package, revealed yesterday in the group's Annual Report, was £1.8 million for the financial year, including a basic salary of £711,000 and benefits of £67,000.
Fankhauser earned a total of £1.2 million the year before, which was down from £4.3 million in 2015 due to the impact of terror attacks affecting travel to Tunisia and Egypt.
His most recent bonus was scaled back after concerns were raised by shareholders earlier this year, causing Thomas Cook's share price to dip.
Nearly a quarter of shareholders voted against the group's remuneration plans to award Fankhauser shares worth 200% of his base salary. As a result, Thomas Cook cut the award to 165%.
Swiss-born Fankhauser took over as Thomas Cook chief executive in 2014, joining from Kuoni.