Top of the satisfaction table, compiled from responses from 7,500 regular train users was West Coast main line operator Virgin Trains with a score of 67%.
London Overground was second with 65%, while the London to Tilbury and Southend company c2c and Merseyrail both scored 64%.
Which? who compiled the survey said: "One First Capital Connect customer told us: 'The price has increased and the trains get more and more crowded. I never see any improvements for the extra money I am paying'.
"And a Southeastern passenger said: 'The prices are terrible, the service is bad and trains are often delayed, cancelled and dirty.'."