The 7.54 London North Eastern Railway (LNER) service from Newcastle to London Kings Cross arrived at 10.52 as expected.
The government took back control of the East Coast rail franchise after its private operators Virgin Trains East Coast lost money.
The joint venture between Stagecoach (90%) and Virgin (10%) won the eight-year franchise to run services in between London and Edinburgh in 2014, but in February, Stagecoach’s chief executive estimated total losses at £260m.
Transport secretary Chris Grayling told MPs the East Coast was “not a failing railway” but Stagecoach and Virgin Trains had “got their bid wrong”.
The creation of the London North Eastern Railway (LNER) resurrected the name of the firm which had operated the line and a number of others in the post-First World War period.
It was absorbed into British Railways when the lines were nationalised after the Second World War.
For the first day of operation, the trains were still sporting the livery of the franchise’s predecessor Virgin Trains.
But Sky News understands trains with the new livery are expected to start running in the next few days.
Despite the first train arriving on time, the service did suffer some disruption with several trains cancelled and a few others delayed.
A spokesman said LNER was pleased the first train had arrived at Kings Cross on time but said it was difficult to ensure there would be no disruption.
He said: “It’s been important to make sure there is no difference for customers.
“As with any operating railway, we do occasionally suffer some disruption, but LNER performance is a priority.”
The East Coast service is operated by the Department for Transport through a so-called “operator of last resort” arrangement, while a new public/private partnership is established.
Mr Grayling told Sky News in May he would consider plans “to enable employees to share directly in the success of LNER both as a pure train operator and subsequently as the new partnership”.
The transport secretary said there would be no sanctions against Virgin or Stagecoach for their failures, though Labour and unions criticised the decision to end the £3.3bn contract – saying it amounted to a bailout for the franchise.