Glasgow Central remained the country’s busiest station - and Britain’s tenth busiest - notching up a 2.2 per cent rise to 27m in 2012-13 compared to the previous year.
Central was also second only to Birmingham New Street in being the busiest outside London - a title it has held in the past.
Aberdeen station also saw a big jump in passengers, by 5.3 per cent to 3.3m.
The figures amid continuing passenger growth, with ScotRail’s total up by one third over the last decade and expected to reach 85m this year.
New lines, extra trains - including by other operators such as Virgin - and a resurgence in the economy are among factors.
Haymarket in Edinburgh lost two per cent of its passengers to 2m, but it is likely to have related to disruption caused by the station’s £25 million overhaul, and the figure is expected to bounce back following completion of the main part of the work last December.
Several other stations recorded smaller falls, including Dundee, down by 1.9 per cent to 1.7m, and Stirling and Charing Cross in Glasgow, down by 1 per cent each to 2.2m and 2m respectively.
Queen Street in Glasgow, Scotland’s third busiest station, which is due to have a £104m expansion starting next year, increased by 0.5 per cent to 16.4m.
The figures differ from those compiled by Network Rail because of separate accounting methods, which this week put Queen Street’s total at nearly 20m.