Network Rail has been fined a record £53.1m by the rail regulator for "shortfalls in performance".
The Office of Rail Regulation (ORR) said the firm had fallen "significantly short" of punctuality targets.
It also said Network Rail had failed to deliver on some of its plans to improve its service and did not know enough about the condition of some key assets.
Network Rail said punctuality had suffered from running more services to meet higher demand.
"We accept that we have fallen short of the regulatory targets for train punctuality and that this is, in part, down to our failure to reduce infrastructure faults quickly enough," said the company's chief executive Mark Carne.
"At the same time, the sharp increase in passenger demand has led us to run more trains at peak times, even when we know this will lead to a more congested railway and punctuality targets may suffer."
He said less crowded trains were a key priority for passengers, but providing more trains to ease congestion led to more delays.
The money from the latest record fine will be spent on faster wi-fi for commuter trains across England and Wales.
The £90m plan to provide faster internet - up to 10 times faster than is currently available - should be completed within three to four years.
Commuters will be able to get a connection through equipment installed alongside the track, rather than having to find a satellite signal.
"It is only right that passengers benefit from the fine, which is why we are investing all of it to improve wi-fi on trains," said Transport Secretary Patrick McLoughlin.
"We all know how frustrating it can be to have our phone calls and internet use constantly disrupted by poor signal."
Almost 87% of Network Rail's trains ran on time in 2013-14, against a target of 92%.
The previous highest fine imposed by the regulator was £14m for late engineering works in 2008.
The regulator did, however, note "a number of significant successes" over the past five years.
These included delivering a major rail improvement programme, including modernising train stations such as Kings Cross and Reading and electrifying railways in the north west of England. It also said the company had helped to improve safety at level crossings.
The network carried 1.5 billion passengers in 2013-14, up from 1.2 billion five years earlier.
"Network Rail has been successful in modernising and improving Britain's railways over the past five years, during a period which has seen record numbers of passengers," said ORR chief executive Richard Price.