Ms Eagle highlighted a range of proposals to stop customers feeling like the system is "always trying to rip you off" and said Labour would introduce a "new deal for passengers".
Among the changes is a drive to end the confusion around peak and off-peak tickets, changing the law to make sure passengers are offered the cheapest ticket no matter where or how the buy it, and ending the inflexibility on advance tickets.
Ms Eagle told the Labour Party conference in Brighton: "Let me say this to the train companies - you make hundreds of millions a year, in a system that pays out more in subsidies than you pay back for taxpayers.
"So when fares go up again in January, do the right thing - voluntarily cap fare rises, since ministers won't. Do your bit to ease the cost of living crisis."