By accelerating the jet stream - a high-altitude wind blowing from west to east across the Atlantic - climate change will speed up eastbound flights but slow down westbound flights, researchers said.
The research could have implications for airlines, passengers, and airports.
The study, led by Dr Paul Williams, an atmospheric scientist at the University of Reading in UK, calculates that transatlantic aircraft will spend an extra 2,000 hours in the air every year, adding millions of dollars to airline fuel costs and increasing the risk of delays.
"The bad news for passengers is that westbound flights will be battling against stronger headwinds. The good news is that eastbound flights will be boosted by stronger tailwinds, but not enough to compensate for the longer westbound journeys. The net result is that round-trip journeys will significantly lengthen.
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"This effect will increase the fuel costs to airlines, potentially raising ticket prices, and it will worsen the environmental impacts of aviation," he said.
The average jet-stream winds along the flight route between London's Heathrow airport and New York's John F Kennedy International airport are predicted to become 15 per cent faster in winter, increasing from 77 to 89 km/hr, with similar increases in the other seasons.
As a result, London-bound flights will become twice as likely to take under five hours and 20 minutes, implying that record-breaking crossing times will occur with increasing frequency in future.
Due to the extra time spent in the air, transatlantic flights will burn an extra USD 22 million worth of fuel annually, and will emit an extra 70 million kg of CO2 - equivalent to the annual emissions of 7,100 British homes. This might only be the tip of the iceberg, researchers said.
"The jet stream encircles the globe, and there is one in the southern hemisphere too. It is possible that flights elsewhere in the world will also suffer from a similar jet stream effect," Williams said.