Go-Ahead Group said GTR passenger revenue fell 3% in the first quarter, as it came under pressure from months of strike action linked to planned changes to the role of conductors.
GTR, which runs Southern, Thameslink, Great Northern and Gatwick Express, also saw passenger journeys fall 0.5% between July 3 and October 31 this year.
Go-Ahead, which owns 65% of GTR, booked annual profits of almost £100 million last month, but chief executive David Brown said GTR does not make any money.
The group is expecting to make a 1.5% margin on GTR over the seven-year period for which it holds the franchise.
In its first-quarter update, the firm said: "Our expectations for the full year remain unchanged, with robust trading in the first quarter.
"The group remains in a good financial position, with strong cash generation and a robust balance sheet."
Go-Ahead said passenger revenues for Southeastern and London Midland grew by 3.5% and 8% respectively.
Focusing on GTR's performance, it added: "Passenger revenue and journeys have been adversely affected by strike action during the period.
"As previously reported, the additional resources being invested in GTR to support service delivery continue to impact margins in the short term. Our margin expectations for the life of the franchise remain unchanged."
The update comes as protests were expected to be held in Westminster on Tuesday in the latest twist in the long-running dispute over changes to the role of conductors.
Members of the Rail, Maritime and Transport union will also strike for 48 hours from Friday, with further walkouts planned in the coming weeks, causing travel misery for hundreds of thousands of passengers.
Southern says moving conductors to a new role of on-board supervisor will improve services to passengers, with responsibility for closing train doors switching to drivers.