Govia Thameslink (GTR), parent company of Southern rail, paid £2,233,000 in 2015-16, which it said was about 50% more that in 2014-15.
The company went on to face further disruption this year, with months of strikes in a row over guards' roles and high sickness levels on Southern.
Compensation figures for 2016-17 have not yet been released.
Last December, consumer group Which? lodged a "super complaint" amid claims the system for obtaining compensation for delayed journeys was too complicated.
The rail regulator, the Office of Rail and Road (ORR), also made a number of recommendations to the industry - such as raising awareness of what compensation was available and making claim forms easier to understand.
Independent watchdog Transport Focus has found the proportion of people claiming compensation has nearly trebled over three years, from 12% in 2013 to 35% this year.
The ORR's deputy director for consumers, Stephanie Tobyn, called for continued progress and said: "More needs to be done."
Rail minister Paul Maynard said: "Passengers need to know that they will be compensated fairly.
"We have been working with partners in the rail industry to ensure passengers are aware of their right to recompense for disruption and, at the same time, we are making the claim process simpler and swifter so that it is easier and more attractive to apply."
Data released by the government and Network Rail also showed GTR received more than £22m from Network Rail in compensation for disruption, but GTR said those payments had gone to the government.
The Rail Delivery Group, which represents train operators, said Network Rail's payments were "entirely separate" from those made to passengers.
The net payment received by the rail company from Network Rail was £22,444,616.71.

The Lego Movie creators Chris Miller and Phil Lord and Fox 21 TV Studios have optioned the rights to the podcast, reports Deadline.
They are developing a series which will chronicle the making of the podcast as it follows a new case.
The first series, a spin-off of NPR's This American Life, followed the murder of Hae Min Lee and the ex-boyfriend jailed for her death.
It became a cultural phenomenon, topping the iTunes chart for several weeks and picking up a Peabody Award.
Co-created and co-produced by Sarah Koenig and Julie Snyder, and hosted by Koenig, they will both act as executive producers on the forthcoming TV show.
"Chris (Miller) and Phil (Lord) take an unexpected approach to telling stories and that is so appealing to us at Serial," Snyder said.
"They experiment. They don't mimic formulas. Developing a show with them is exciting because we feel like we speak the same language, only they're smarter than us."
"From the very first week of Serial's release last fall, everyone at Fox 21 TVS was obsessed with the podcast," explained Fox 21 TV Studios president Bert Salke.
"One year later, thanks to the incredible passion of Chris and Phil, who flew to New York and shared their vision with Sarah, Julie (Snyder), Alissa (Shipp) and Ira (Glass) for what the series could be, we're moving forward on this exciting project...we are confident we'll attract a spectacular writer and look forward to pitching it to outlets very soon."
The Serial podcast has been commissioned for two more seasons.
Series two will concentrate on the story of captured US Army soldier Bowe Bergdahl, and will air in the autumn.
Lord and Miller have also signed on to direct the Han Solo Star Wars movie, which is set for release in May 2018.
A troubled rail firm paid over £2m in compensation last year for disruption to passengers, figures have shown.
[NEXT_CONCEPT]
Popular true crime podcast Serial is set to become a cable TV series.