Govia Thameslink Railway (GTR) have been fined £13.4m for poor performance on Southern Rail, the Department for Transport has announced.
The government said the fine would have been higher, but most of the delays had not been Southern’s fault.
The DfT said strikes and unprecedented levels of sick leave were also to blame.
A spokesman for GTR said the company accepted the fine as a “fair outcome”.
He said: “The settlement acknowledges that the industrial action taken by the trade unions has been a major contributor to the disruption experienced by passengers in the past year, and we welcome the fact that a significant proportion of our claim was recognised.”
GTR said it had agreed to invest the money on “driving up operational performance”.
Charles Horton, the company’s chief executive, said “We are pleased that this issue has been concluded, and accept and are sorry that our service levels haven’t been good enough for passengers.”