An estimated 14 million passengers travelled through in the year to the end of March, according to the Office of Rail and Road (ORR).
The east London station is a key interchange, enabling people to connect with other transport routes.
Waterloo was knocked off the top spot for the first time in 17 years due to the pandemic.
Just 12.2m people used the station in 20220/21, down from 86.9m a year earlier.
Passenger numbers across Britain dropped by 78 per cent over the last 12-month period.
However, London’s railway stations still dominated the top ten most used.
London Victoria was heavily relied on during the pandemic with 13.8m entries and exits, followed by London Bridge also with 13.8m.
London’s #Stratford railway station recorded the most passenger entries and exits with 14 million in 2020-21 - a year that saw Britain’s passenger usage drop 78% compared to the previous year.
The numbers are revealed in our #StationUsage statistics▶️ https://t.co/2fFwq0u5q8 pic.twitter.com/xJOeaajXDC
— ORR (@railandroad) November 25, 2021
London Liverpool Street also made the top five most-used stations in Britain with 11.2m.
Highbury and Islington, 8.7m, Clapham Junction, 8.4m, Barking, 6.7m, and East Croydon, 6.7m, entered into the top 10 for the first time.
They replaced more central stations including London Paddington, London Euston, London St Pancras International and London Kings Cross.
It underlines their importance as vital stops and interchanges, linking keyworkers to key transport networks.
Six stations had no passengers, mainly due to services being suspended because of the virus crisis.
ORR’s figures also show Birmingham New Street as the only station outside of London that recorded more than 6m entries and exits, with 7.4m people travelling from or to the station in 2020-21.
Liverpool Lime Street, 3.5m, and Cambridge, 2.3m, were the only stations included in the top 10 most used stations outside of London that did not appear last year.
These two stations replaced Gatwick Airport and Glasgow Queen Street.
Only five railway stations in Great Britain had more than 10m entries and exits in 2020-21 compared with 43 stations in 2019-20.
Nearly 200 railway stations across Britain had fewer than 1,000 entries and exits, with six recording no entries or exits during the last year as a result of services temporarily suspended at the majority of these stations due to the pandemic.
There were 18 stations with less than 20 and 59 with less than 100 recorded entries in 2020-21.
“Throughout 2020-21 the railways remained an essential service for those people who needed to travel during a year which was impacted by the pandemic,” said Feras Alshaker, ORR director of planning and performance.
“We’ve seen a radical change, especially in London, in the stations people were using the most.
“This year we have seen many railway stations with very few passenger entries and exits.
“However, we know that recent figures show leisure journeys are nearly back to pre-pandemic levels, while there has been a slower increase in commuter journeys.”