Frank Meysman, a former US consumer goods executive, took over as chairman of the troubled tour operator last month and was expected to begin with a boardroom cull.
Among the departures are City grandees Bo Lerenius and Peter Middleton, who will retire early to allow Meysman “more flexibility to refresh the board”, the company said in a statement.
David Allvey, who was due to retire after nine years service, will also leave together with Middleton and Lerenius at the time of Thomas Cook’s annual general meeting on 8 February.
A fourth director, Roger Burnell, will step down at the annual general meeting in 2013.
The news came as Thomas Cook revealed that its former chief executive Manny Fontenla-Novoa received a £1.17m payoff from the company after he resigned in August despite presiding over a spate of profit warnings, which led to a bailout by its banks last month.
Fontenla-Novoa received the payout on top of the £1.19m salary earned in his last year of employment, according to the firm’s annual report.
Shares fell 3.23 per cent to 15p.