As cuts to air passenger duty (APD) are set to encourage new and cheaper domestic flights from 1 April, the consumer group said train travellers are already paying a premium on many routes.
Which? carried out research to find the cheapest available options for travelling by train and by plane over the Easter break on 10 UK routes, and assessed the carbon emissions for each option.
It found plane journeys emit twice the CO2 on average (118% more) when compared with travelling by train, while train tickets are 35% dearer. Just three out of 10 routes are cheaper by train.
The starkest difference in price was for the Edinburgh to Bournemouth route, a journey which costs 239% more to complete by train.
The cheapest return rail fare available costs £127, even when using split ticketing on the outward journey and an advance fare for the return. In contrast, the return flight costs £38.
A flight on this route emits an average of 218kg of CO2 per person, 131% more than travelling by train.
The only other two journeys found to be cheaper by rail were on the Edinburgh to Newquay route, and the Bristol to Aberdeen route.
The former costs 13% less at £250 for a return fare, but would take more than seven times as long to complete, with a total return journey time of 22 hours and 2 minutes.
The Bristol to Aberdeen route meanwhile costs more than a fifth less by rail (21%) but takes 18 and a half hours for a return trip, more than six times as long as by plane.
Rory Boland, Which? travel editor, said: "As travellers become increasingly concerned about the environmental impact of their journeys, many face a difficult trade-off between the price of their ticket and the cost to the planet, with just three out of 10 journeys we looked at working out cheaper by rail."
