The British airline, owned by Europe's biggest tour operator TUI Travel, has said it planned to operate the flight from Birmingham to Palma on July 28 once final safety clearance was received.
Weekly flights to Spain using biofuel will begin in September for a year, on the same route initially and switching to Birmingham-Alicante during the winter schedule.
Thomson said the flights would operate on a 50/50 blend of Jet A1 fuel and hydroprocessed esters and fatty acids (HEFA) fuel - made from used cooking oil - in both of the plane's engines.
Dutch airline KLM operated the world's first scheduled biokerosene-powered flight on Wednesday after one of its Boeing 737-800 jets flew 171 passengers between Amsterdam and Paris, using the same cooking oil-Jet-A mix that Thomson plans to use.
Thomson managing director Chris Browne said: "As sustainable biofuels become more commercially viable, Thomson Airways plans to expand its use of sustainable biofuels across its fleet over the next three years."