The managing director of Avanti West Coast is stepping down, the company has announced, amid a backlash over timetable cuts.
The rail firm said Phil Whittingham would leave on 15 September - the same day new train strikes will take place.
Services between London and Manchester have been cut to a third, with the company blaming "staffing issues".
Manchester Mayor Andy Burnham said the firm should be in the "last chance saloon".
Mr Burnham has previously called for the company's licence to be revoked if services aren't restored - a decision only the government can take.
"This is England's most important railway line, linking its biggest cities, and every day that this chaos continues is a day when our economy in Greater Manchester is damaged and another day of misery for passengers," he told the BBC's Today programme.
Last month, Avanti West Coast cut its timetable from three services an hour to one - blaming staffing issues.
Explaining the timetable change at the time, Mr Whittingham said the "current industrial relations climate" had resulted in "severe staff shortages in some grades through increased sickness levels, as well as unofficial strike action by Aslef members".
The company said it currently had more drivers than before the pandemic but relied on staff working overtime in order to run a full timetable and keep up with training.
The union said the company needed to employ more drivers - and denied any accusation of unofficial strike action.
In a statement, Avanti apologised to customers for the "enormous frustration and inconvenience" caused by the reduced timetable.
The cuts to the timetable have prompted widespread criticism and frustration.
Mr Burnham said Mr Whittingham's departure revealed a serious management failure, and urged the government to "stop playing politics" regarding the country's widespread strike action.
He called on the UK's new prime minister, who will be announced on Monday, to "reset" the debate.
"We need to start fixing problems and working together, rather than this playing the politics and trying to demonise the trade unions."
A spokesman for the Department for Transport said: "People deserve certainty and confidence that their train will run on time, and while the change of schedule was unavoidable, it should minimise the fallout for passengers.
"This is a prime example of why we need to modernise our railways, so passengers benefit from reliable timetables that don't rely on the goodwill of drivers volunteering to work overtime in the first place."
First Rail boss Steve Montgomery said: "Having led the team through the challenges presented by the pandemic over the last two years and into the recovery period, Phil leaves with the team ready for the challenges in delivering the future service requirements.
"I would like to thank Phil and wish him well in the future."
On Wednesday, Aslef said its members at 12 operators - including Avanti West Coast - would take industrial action on 15 September.
Separately, the RMT union has announced two more national rail strikes later this month. Workers will walk out on 15 and 17 September in a long-running dispute about pay, jobs and conditions.