Protests were held outside around 40 stations to mark the biggest increase since 2013.
Regular rail users are paying almost 5 times more than commuters in Europe today's research showed, which coincides with a hike in rail fares of almost 4 per cent.
Some commuters saw their season tickets increase by around £100 a year.
A spokesperson for Virgin Trains on the East Coast route could not say how much the season ticket had risen by, but a commuter told the Peterborough Telegraph that his season ticket a year ago cost £7,484, approximately 3.6 per cent less than the new figure.
A year's season ticket going from Aylesbury into London, with tube travel, is now around £4,400.
On the travel firm's website the carrier says its staff realise that nobody wants prices to rise but the extra money is need for upgrades on the network.
Labour's shadow transport secretary met party campaigners at Stevenage railway station this morning to slam rail fare rises - before his train north for more demonstrations broke down.
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This will ensure it is known how best to make use of existing trackside infrastructure and utilise Network Rail assets, as well as testing suitable track-to-train radio systems to deliver services to passengers under real-life conditions.
"What's good enough for motorists should be good enough for rail passengers".
Greater Anglia's fare rise is exactly in line with the national average which is set by the government and based on July's inflation rate. 60 per cent of people said earlier this year that trains should be publicly owned.
London mayor Sadiq Khan said: "It is simply not right that millions of rail passengers face eye-watering fare hikes today after suffering 12 months of delays, cancellations and disruption".
So despite train companies nearly doubling the number of cheaper Advance fares in recent years, passengers will need to be quick to get the best choice of deals.
"For every pound paid in fares, 97p goes directly back to operating and improving services and, with more people travelling, that means more money for investment by the private and public partnership railway to build the better network Britain needs".
But the 2017 European Railway Performance Index found the highest-ranking countries included those with high government subsidy of rail fares, with Germany and France outstripping Britain.