The Office of Rail Regulation (ORR) has slapped a £53.1m fine on Network Rail because it fell "significantly short" of punctuality targets.
According to the train sector watchdog, Network Rail was guilty of a range of "shortfalls in performance" and failed to deliver on supposed plans to improve its service.
"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 Mark Carne, CEO at Network Rail.
"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."
The network carried 1.5 billion passengers in 2013 to 2014, up from 1.2 billion in 2009.
Network Rail's fine is more than three times the amount it paid in 2008 for late engineering works. Between 2013 and 2014, 87% of Network Rail's trains ran on time, however its target was set at 92%.
Despite the fine, ORR chief executive Richard Price said that Network Rail has improved some of its infrastructure.
"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 Price.
Network Rail's "successes" include modernising train stations such as King's Cross and Reading and electrifying railways in the north west of England.