Passengers were stuck in cold and dark carriages for hours recently after overhead electric cables were damaged.
Network Rail’s managing director for the Wales and Western region, Michelle Handforth, has resigned.
The news came just days after infrastructure problems left hundreds of passengers stranded in carriages for hours in the dark in west London.
Ms Handforth was paid a £330,000 salary and commuted to work from Aberdeen.
A rail insider said she had made the decision to resign before the west London incident, after recognising the challenges of the role.
Earlier this month, passengers were stuck in cold and dark carriages for hours when overhead electric cables were damaged in Ladbroke Grove.
Elizabeth Line, Great Western Railway and Heathrow Express trains were all affected, with some passengers trapped for more than three hours with no access to toilets.
Multiple rail system faults and damaged rails had caused problems on Paddington services in the weeks before the incident.
Ms Handforth had been in the role for three-and-a-half years.
Before joining Network Rail, she was chief executive officer for the Port of Aberdeen.
Maryam Eslamdoust, general secretary of the Transport Salaried Staffs’ Association (TSSA) said one person resigning “simply isn’t enough”.
She urged Network Rail needed to invest properly “in the maintenance of its infrastructure”, saying delays to repairs and maintenance caused cancellations and increased safety risks.
“Ultimately though, this all goes back to the government who set the budget that Network Rail have to work with,” she said.
The TSSA says nearly 500 staff who work on replacing old rails and sleepers face losing their jobs under Network Rail plans to cut costs.
But the campaign group Railfuture, which represents passengers, said Ms Handforth’s resignation was a welcome show of responsibility.
“We certainly support the notion there is accountability at the top of the rail industry,” said the group’s spokesman Bruce Williamson.
“And it’s also important that the people who are recruited to run our railway are the people with the right set of skills to deliver the railway that we all want to see.”