Which? asked more than 10,000 train passengers to rate their train service over the past year across 30 train companies.
Southeastern has an overall customer satisfaction rating of 41 per cent, Thameslink came in at 36 per cent and Southern was 34 per cent.
The only rail operator ranked lower was Northern at 32 per cent.
Alex Hayman, Which? managing director of Public Markets, said: “It is shocking that a modern transport system is allowed to have such a negative impact on the people who rely on it every day. Its failures are affecting people’s health and employment, and some are even forced to move home as a result of the disruption.
“If the Government rail review is to have any hope of restoring faith in the system it must listen to passengers, who have too often been an afterthought.
“However, train companies should not wait for the results of the review to take action. The industry must start putting the interests of passengers first to address the chronic issues identified in our survey.”
The results, which were published on Friday (January 25) showed half of commuters (48 per cent) in Which?’s annual rail survey say they find travelling by rail frequently stressful, with some people even reporting that they have had to move house to escape a nightmare train journey.
The consumer champion spoke to commuters about the impact delays had on their lives. Issues included missing out on time with family and friends (17 per cent), being disciplined at work (nine per cent) and additional childcare costs (six per cent).
Four per cent of respondents, equating to more than 100 commuters, said they even had to move house as a result of the disruption.
Ross Powell commutes into London every day on both Southern and Thameslink trains from his home in Horley.
He’s worried about the long-term impact Southern’s continued poor performance might be having on local house prices, and even his job prospects.
He said: “I’ve been asked in a few interviews for possible jobs where I live and get a lot of comments along the lines of ‘Oh, I hear the trains from there are terrible’.”
In response to the findings by Which? a Govia Thameslink Railway spokesperson said: “Passengers are benefiting from improved services on what are the UK's busiest rail routes.
“Punctuality and reliability are back on track on Thameslink and Great Northern after last May's timetable change - and Southern services, which were unaffected, are 15 per cent more punctual than a year ago.
“We are now running 400 more services every day than we were a year ago with space for 50,000 more commuters to and from London.
“This May we'll be adding still more trains into the timetable, and on Great Northern we are about to replace Britain's oldest electric trains with a brand new air-conditioned fleet.
“Passengers affected by the May timetable have been paid £17million in compensation and we have set aside a £15 million fund dedicated to making improvements customers tell us they want.”
Another survey, published today (January 29) shows passenger satisfaction with rail services has fallen to a 10-year low.
Independent watchdog Transport Focus released the results of its National Rail Passenger Survey, and it said overall satisfaction with rail services in the UK was 79 per cent, the lowest level since 2008.
Anthony Smith, chief executive of Transport Focus, said: “Our latest survey confirms passenger satisfaction has fallen to a 10-year low. Government and the industry must continue to focus on performance. In the longer term the Government’s Rail Review must bring about fundamental change.
“Passenger irritation at poor performance erodes their most basic trust in the industry. Passenger frustration at continual fare increases saps confidence in the system to reform itself. Passenger anger during the summer timetable crisis was palpable.
“A better value for money and more reliable railway must arrive soon for passengers.”
The report comes after a survey of more than 25,000 passengers between September 1 and November 16 2018.
Commenting on the results of the Transport Focus survey, Alex Hayman, Which? managing director of Public Markets, said: “These worsening levels of satisfaction, including dire commuter ratings for value for money, mirror our own findings – which show passengers are suffering with stress, having issues with their employers and even moving homes due to appalling disruption on the railways.
“If the Government rail review is to have any hope of restoring faith in the system it must listen to passengers, who have too often been an afterthought. But train companies should not be waiting for the outcome of the review to address the chronic issues experienced by passengers.”