Merseyrail returned to the black and its turnover rose in 2021 as it entered a "recovery phase" following the impact of the Covid-19 pandemic.
The company has posted a pre-tax profit of £2.7m for the 12 months to January 8, 2022, after it fell to a loss of £2.5m during the prior year.
Its turnover also grew from £150m to £163m over the same period.
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The figures compare to a turnover of £175.1m and pre-tax profit of £18.1m in the year before the pandemic struck.
A statement signed off by the board said: "The pandemic has had a significant impact on the group's operations, with passenger journeys reducing up to 90% during the height of the pandemic.
"These numbers have since improved, however, we continue to operate 16% below pre-pandemic levels.
"The directors are content with the performance of the business in the year given the continued impact of the pandemic."
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Merseyrail added that following the pandemic, in which is sought cost savings, it is now "moving to a recovery phase" and its focus is on bringing passengers back to the network.
Merseyrail said a programme of upgrade work to extend platforms and carry out signalling work continued during the year and is expected to be completed in the third quarter of 2023.
On its future, the business said: "Throughout FY 2023 Merseyrail will continue, in partnership with Merseytravel and others, to make improvements to the network and service.
"The new fleet expansion and procurement of a battery-operated unit to enable class 777 services to be extended off the current Merseyrail network will support in our commitment to upgrade services for our customers.
"Despite the challenges relating to the introduction of the new fleet into service, real progress has been made in many areas with train testing on the Merseyrail network now well advanced, and power supply upgrades due for completion in FY 2023.
"Although the pandemic had a negative impact on our revenues and the business sought to cut costs, the business is now moving to a recovery phase which has so far been strong.
"We are seeing a positive trend in passengers returning to the network, revenues and cashflows are monitored daily and we anticipate impacts to EBIT as a result of consequences following the pandemic will be minimal during FY 2023."
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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.