Some peak times trains are carrying more than double their capacity as the network strains under demand, official figures have revealed.
Southern Rail's 7.16 East Grinstead to London Bridge service is the UK's worst offender, running at 213% of capacity, according to the Department for Transport data.
This meant 1,366 passengers were on the train with space for 640, as it came into the capital from West Sussex.
Other jam-packed trains include the TransPennine Express' 16.00 from Manchester Airport to Edinburgh running at 187% capacity and Thameslink's 17.08 from Sutton to St Albans at 194% of capacity.
Overall, the average proportion of passengers carried on overcrowded trains in major cities was 3.8%.
The survey covers England and Wales and is based on standard class passengers travelling on weekday services in autumn last year.
Lianna Etkind, from the Campaign for Better Transport, said overcrowding was making passengers' lives a "misery".
"People are rightly angry that they pay more in fares year after year, but never get a seat, and have to stand crammed into someone else's armpit," she said.
Transport Focus chief executive Anthony Smith added: "Continuing to invest in new trains, better frequency, track capacity and improved signalling will ultimately give passengers a better chance of getting a seat or at least standing in some comfort, able to do something other than endure.
"In return for continuing fare rises passengers expect continued investment and improvement."
The transport secretary, Chris Grayling, signalled last week that he was planning to scrap first-class carriages on more commuter trains in an effort to ease overcrowding.
Half of daily arrivals into London are in the morning peak, whereas in other cities this figure is around one-third. More than 583,000 passengers travel into the capital every morning by train, compared to 42,000 in Birmingham.