The impact of the Covid-19 pandemic forced Merseyrail into the red during 2020 as passenger numbers slumped by up to 90% during lockdown.
New documents filed with Companies House show the company fell to a pre-tax loss of £2.5m for the 12 months to January 9, 2021, compared to a £18.1m profit in the prior year.
Its turnover also declined from £175.1m to £150m over the same period.
Before the pandemic, Merseyrail operated more than 600 train services from Monday to Saturday and 340 on Sundays.
A total of 110,000 passenger journeys were made each weekday and 30m every year.
Because of Covid-19 restrictions, passenger journeys dropped up to 90% during lockdowns and Merseyrail reduced the number of trains per day to about 350.
A statement signed off by the board said: "Since the start of the Covid-19 pandemic, the directors have closely monitored the results of the group and the impact the pandemic has had on UK public transport and the wider economy.
"Whilst the impact of Covid-19 evolves we continued to consider several scenarios and the impacts on passenger revenue, costs, profits and cash flow.
"Since the start of the first national lockdown for the UK, passenger revenue has fallen dramatically.
"This had started to recover slightly from mid-2020 with the easing of the national lockdown, however, passenger revenue was much lower than what it was in 2019 and the directors continue to monitor passenger revenue on a daily basis.
"The fall in passenger revenue has had a significant impact on the results of 2020.
"Although the group did not furlough any employees, there have been strict cash saving measures implemented in order to counter some of P&L impacts of Covid-19 as well as preserving cash reserves."
Merseyrail was awarded a 25-year deal in 2003 to provide rail services on behalf of Merseytravel and has two 50% shareholders, Serco Group and Abellio.
It has 68 stations, with terminus sites at Southport, Ormskirk, Kirkby and Hunts Cross on the Northern line and New Brighton, West Kirby, Chester and Ellesmere Port on the Wirral line.
Merseyrail was contacted for a comment.
