Charges of up to 50p across 10 stations nationally will be abolished next year despite bringing in Â£20.3m for Network Rail between 2013/2014 and 2016/2017.
Network Rail charges 40p for access to the toilets near the New Station Street entrance at Leeds, generating an average of Â£688 per day in the process.
Such charges have been unpopular with passengers, and after consultation, chief executive Mark Carne said they would no longer have to rummage for change.
It currently costs between 30p and 50p to use the toilet at 10 large stations across the UK, including London’s Euston, Kings Cross, Liverpool Street, Paddington and Waterloo, Manchester’s Piccadilly, Edinburgh’s Waverley, Glasgow Central, Liverpool Lime Street and Leeds.
Mr Carne, who is stepping down this year, told The Times newspaper: “As a customer organisation I think it is quite wrong to penalise people when they are in discomfort. Our job should be to make their life easier, not more difficult. We want to treat people with dignity and respect.”
Anthony Smith, chief executive of traveller watchdog Transport Focus, said: “This will be really welcomed. It is a key priority for improvement of stations according to our research and will signal the end of fumbling around in your pocket for change to spend a penny.”
The charges have already been scrapped at London Victoria, which made more than Â£900,000 from the charge last year. Average ticket prices on mainline trains went up by 3.4 per cent this year – another hike to add to a 64 per cent rise in real terms since 1980.