Punctuality figures published by Network Rail show Virgin Trains, which runs Glasgow-to-London routes, ranked bottom of the UK's 19 franchised operators in the four weeks to January 5, when nearly one- quarter of services arrived more than 10 minutes past their scheduled time.
East Coast, which operates regular services from Edinburgh, Aberdeen and Inverness to London, fared little better, with only 77% of trains recorded as on time over the same period.
Network Rail, which operates the UK's track and signalling infrastructure, said heavy rainfall had been a factor in delays as services were hit by floods, landslides and embankment slips.
Engineering over-runs scheduled over the Christmas holidays on the West Coast Main Line also contributed to Virgin's problems, together with failures of points and signalling equipment.
Virgin has called for dramatic performance improvements on the route, the main artery connecting London to Scotland, which has been beset by problems despite completion of a £9 billion upgrade in 2008.
Overall, a total of 88.2% of trains ran on time over the four-week period, compared with 88.8% in the same period over the festive period of 2011/12.
Nine of 19 firms achieved at least 90%, with ScotRail having 91% of services arrive within five minutes of scheduled times.
A spokesman for Network Rail, which is halfway through an investment programme, said: "Severe weather with multiple flooding, landslide and embankment slip events caused severe disruption over a number of days to many train operators and particularly impacted our long-distance customers."