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.
A troubled rail firm paid over £2m in compensation last year for disruption to passengers, figures have shown.