Former rail minister Claire Perry quit the Government just one day after telling MPs she did not believe falling on her sword would help resolve problems with services provided by Southern Rail.
Ms Perry resigned on Thursday evening and no reasons have been given for her departure from the Department for Transport.
The Tory MP for Devizes had faced increasing pressure in recent weeks over cancelled and late running trains on routes in the south-east of England, with London Mayor Sadiq Khan calling on the Government to strip Govia Thameslink Railway (GTR) of its franchise.
MPs grilled Ms Perry on the issue during a Westminster Hall debate on Wednesday afternoon.
She admitted she had repeatedly thought about quitting over the failures of Southern Rail but thought it would not help.
She said the current situation "feels like a failure'' but insisted stripping GTR of the franchise would not make problems disappear.
She said: "At the moment I do not have the levers to pull to take the franchise back.
"So what are we going to do? If I thought it would help by me falling on my sword, I would.
"I've thought about it repeatedly. I don't like failure, I don't fail at stuff in my life, this feels like a failure."
Southern Rail is involved in an ongoing dispute with the Rail, Maritime and Transport (RMT) union over plans to transfer responsibility for closing train doors from conductors to drivers.
Services have been hit by industrial action and high levels of staff sickness.
The company has been using a revised timetable since Monday, cutting 341 trains a day.
The issues surrounding Southern services are likely to be some of the most pressing faced by newly appointed Transport Secretary Chris Grayling.