Only Birmingham New Street and Glasgow Central carry more passengers than Leeds, which handled 29,723,734 entries and exits in the last year.
Sheffield, with just over 9m travellers, is Yorkshire’s second busiest station, followed by York, Huddersfield and Doncaster.
In contrast, the quietest station in the county is Hensall, near Selby, with an annual throughput of just 544 people.
London Waterloo recorded the most journeys in the 12 months to March 31 at 99.1 million, the Office of Rail and Road said.
The 10 busiest stations in Britain are all in London apart from Birmingham New Street, which is seventh on the list.
In Scotland, Glasgow Central remains the busiest station with passengers using the hub 30 million times in 2015/16, with Edinburgh in second place at 21.7 million.
Cardiff Central is the busiest station in Wales with 12.7 million journeys.
There were more than 2.9 billion entries and exits at all rail stations in Britain in 2015/16, an increase of 5pc compared with the previous year.
The Rail Delivery Group, representing train operators and Network Rail, said the figures demonstrate the need to “invest and plan long-term for increasing demand”.
The Yorkshire region’s busiest stations (annual passengers)...
1. Leeds: 29,723,734
2. Sheffield: 9,213,092
3. York: 8,848,652
4. Huddersfield: 5,041,600
5. Doncaster: 3,751,802
... and the quietest:
1. Kirton Lindsey, North Lincolnshire: 200
2. New Clee, North East Lincolnshire: 458
3. Hensall, Selby: 544
4. Rawcliffe, East Riding of Yorkshire: 800
5. Wressle, East Riding of Yorkshire: 912