Thomas Cook surcharges will vary from £15 to £40, depending on the length of the flight, and come into effect on all new bookings made with Club 18-30, Airtours, Sunset and Thomas Cook sub-brands.
Fuel prices have risen 40% in the past year, and are likely to increase further as the unrest in Libya spreads.
Thomson customers will be hit by similar price increases on flights and packages from Friday.
Ian Ailles, chief executive of Thomas Cook, said: "We've worked hard to keep the impact of the rising fuel costs on our holidaymakers to a minimum, but the fuel levy is an unavoidable result of the rising price of oil."
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