All the top 10 busiest stations reported an increase in passengers in 2012/13 and the number of people using stations across Britain in this period rose 3.3%, the statistics from the Office of Rail Regulation showed.
Passenger numbers at Glasgow Central, the busiest in Scotland, rose 2.2% to 27.18 million during the past financial year.
Based on the estimated number of exits and entrances to a station during 2012/13, Waterloo in London was the busiest station, with numbers, compared with 2011/12, rising 1.9% to almost 96 million.
Second was Victoria in London, with numbers rising 1.6% to 77.34 million, with another big London terminus, Liverpool Street, third with a 2.4% rise to just under 58.45 million.
It has meanwhile emerged that the compensation bill for work at Queen Street Station in Glasgow could run to tens of millions of pounds.
Network Rail has to pay out to train operators every time a track is closed and the maintenance work on Queen Street's main tunnel is expected to last up to four months with no services able to run into the seven platforms.
Some trains, such as Edinburgh services, will be diverted to Central Station and others to the low level platforms but not all services will be able to operate.