First Scotrail, which is responsible for 95% of train journeys in Scotland, ran 83.6% of services on time compared to 88.2% for the same period last year.
East Coast, which runs services from Edinburgh to London King's Cross, was up slightly from 76.7% to 78.6% while Virgin, which runs services from Glasgow to London Euston, was almost unchanged with 79.5% punctuality.
Rail services in the south of England saw the biggest dip, which was blamed on the severe winds on the St Jude's day storm.
London Midland achieved an on-time punctuality figure of only 76%, Network Rail reported.
Overall, companies nationwide ran 84.4% of trains on time between November 10 to December 7.
This compared with a figure of 85.4% in the corresponding period in 2012 and was also down on the rolling 12-month average of 90.4%.
Apart from London Midland, companies that ran fewer than 80% of trains on time in the latest four-week period were East Coast (78.6%) and Virgin Trains (79.5%).
The majority of delays were attributable to Network Rail because they involved factors such as fatalities on the line, trees and other debris blocking the tracks or overhead power line failures due to the bad weather.
The best-performing company in the latest period was c2c with a figure of 97.3%. Only London Overground (94.8%), Chiltern (93.6%) and Merseyrail (90.5%) managed to run more than 90% of trains on time.