The Overlander train service between Auckland and Wellington will cease at the end of September.
Toll NZ blamed continual loss of patronage.
It said the service, which had run at a substantial loss for many years, faced increased costs and competition from cheaper travel options and was no longer viable.
Full one-way fares are $170, although winter specials are advertised at $99.
In November 2004, the company ended the overnight train services between Wellington and Auckland.
The service, which started on Valentine's Day 1909, had been outpaced by cheap flights and the convenience of cars, the company said at the time.
In March last year, the company cut several North Island towns from The Overlander's schedule.
Corporate affairs manager Sue Foley said then that in some places the numbers of passengers were so low "we could not justify keeping it [the service stop] going".
Toll NZ chief executive David Jackson said yesterday the company was well aware of how New Zealanders felt about passenger rail and had approached the Government to see if they could assist with the continued operation of The Overlander service.
"After working through with the Government, both parties concluded there was not the passenger numbers to justify keeping it running. Significant investment would also have been required to replace the ageing carriage fleet."
Mr Jackson said there was certainly a place in New Zealand for tourist trains such as the Tranz Coastal and Tranz Alpine in the South Island.
"These are shorter journeys that people can easily manage in a day and fit in other activities."
In April Mr Jackson said in a statement to the New Zealand Stock Exchange the company was seeking expressions of interest in the Tranz Coastal and the Tranz Alpine.
He said the services would only be sold if the right buyer could be found, otherwise Toll would continue to operate and grow and enhance the services in the South Island.
The Green Party said the Government must ensure that Toll did not dismantle the infrastructure that would allow the service to be reinstated when the effects of the end of cheap oil really started to bite.
The last train will run on September 30.