Fines of £20 fines or double the cost of a single fare - whichever is the greater - will be introduced on routes across the region before the end of March.
Stations on penalty fare routes will have either ticket offices or ticket vending machines so customers will have the opportunity to purchase tickets before they travel.
Northern has come under fire over the past year for its record on cancellations, industrial action, overcrowded trains and increased fares.
A Northern spokesman said: “Penalty fares have been in place across the UK rail network for many years, and were introduced to Northern’s routes last year with a trial in West Yorkshire. That trial was well received by customers and even some who were originally sceptical praised the way in which it was been introduced and managed.”
If ticketing facilities are not available at stations, or if offices are closed or machines out of order, customers will still be able to buy a ticket from the on-board conductor.
When customers want to pay cash, but ticket machines are card only, they will be able to obtain ‘promise to pay’ notices from the machines which can be presented, along with cash to the conductor – the full range of fares will still be available on board.
Passengers can also purchase tickets via Northern’s app.