A total of 83.7 per cent of trains ran on time in the four-week period from December 8 2013 to January 4, 2014, Network Rail (NR) said.
This compared with a figure of 88.3 per cent for the same four-week period in 2012/13.
East Coast, which links Leeds and York with London, was the third worst performing, and saw just 76.9 per cent of its trains run on time during the period.
The worst-performing company in the most recent four-week period was Southern, where many fallen trees, as well as landslips on the Brighton line, meant that the company was only able to run 73.1 per cent of trains on time.
The next worst-performing company in December 2013 was First Capital Connect followed by Southeastern and South West Trains.
The best-performing company in December 2013 was London Overground followed by c2c and Merseyrail.
Delays attributable to NR – including external factors such as fatalities, which made up around 20 per cent of all delays – accounted for 60 per cent of delays nationally during the period.
NR said: “A succession of tumultuous storms tested the rail industry’s resilience during a very difficult period.
“During this period, the railway dealt with multiple and sustained extreme weather conditions.
“Storm-force winds brought down almost 400 trees on to the railway while torrential rain caused almost 130 floods and 29 landslips, some blocking major routes.
“Thousands of railway staff responded with dedication and professionalism to repair the damage caused.”
NR added that “despite these considerable challenges” it had, over the same period, successfully delivered a £110m investment programme of improvement work involving many engineering projects – the largest ever undertaken over a two-week period.