Passenger fares on the Capital Connection train service between Wellington and Palmerston North will increase by 5% to 10% from 1 May.
KiwiRail said on Monday the increase is a step towards lifting the viability of the service.
It is the first since November 2011.
KiwiRail recently announced it would continue the service for another two years.
Passenger general manager Deborah Hume said daily patronage needs to increase by 61 passengers in each direction for the Capital Connection to break-even by 2015, and average tickets prices need to be 40% higher.