The 6.07am service, the first train of the day, is to be scrapped as part of the plans which also see evening journeys between Leeds, Harrogate and Knaresborough reduced.
Commuters heading to London will use the early services as they are able to reach the capital before 9am, but Northern says not enough people are using the route and that savings must be made.
Further cuts to services, set to come into force on Sunday, May 15, include the 7.29pm and 9.39pm services on the Leeds - Harrogate - York line. This means a two hour, 10 minute gap between 9.29pm and 11.39pm services between Leeds and Harrogate. The 9.13am, 6.47pm and 9.44pm services from Harrogate to Leeds will also be removed in May. The 9.29pm train will be the last to stop at Knaresborough.
As of December 2021, Northern had already reduced its timetable due to the Covid pandemic.
It then implemented further cuts in January 2022 in what it said would be a short-term measure due to the Omicron variant.
However, in a further blow to commuters, Northern has now announced that it will not only retain the twice reduced January timetable until December 2022, but it will also make even more cuts to services from May this year - meaning there is no longer any way that Harrogate commuters can travel by train to London and arrive before 9am.
Leeds City Council leader James Lewis (Lab) said: “We are very concerned that these cuts are coming in at a time when trains are getting busier as more people return to working in Leeds city centre, as well as at a crucial time for businesses in the night time economy as they recover from the impact of the pandemic.
“We are calling on Northern to commit to returning to a full timetable as soon as possible.”
Three services in each direction on the Leeds - Wakefield Westgate - Sheffield line will also be removed. The 9.48am, 12.48pm and 3.48pm services from Leeds, and the 8.16am, 11.15am, and 2.15pm services from Sheffield will be scrapped.
Services on the Halifax - Bradford - Leeds - Selby - Hull line will be only every two hours, with the 7.17am, 11.15am, 3.16pm, 7.15om and 10.15pm services from Hull; and 9.17am, 1.17pm, 5.17pm and 9.17pm services from Halifax all finishing.
Northern said it is doing its best for customers, but claimed it had to make the changes as fewer passengers were using their services.
A spokesperson for Northern said: “We fully understand the concerns of those using our trains and we are doing all we can to provide the best possible service for our customers who are very much at the heart of everything we do.
“We’re seeing fewer commuters travelling each day, and people travelling at different times of the week and for different reasons. We’ve made decisions about our timetables based on the levels of resource we have available and prioritising the routes with the highest customer demand, and which support the region’s economic growth.
"The timetables currently in place will broadly continue with some amendments from May 2022 and into the Summer."