Ossett Town's 2-0 victory over already relegated New Mills on Thursday night gave them an unassailable lead over Railway in third bottom.
With only three matches left to play, Railway trailed Ossett by 11 points with a mere 26 from 39 matches this season.
Railway will drop into the Northern Counties East League unless they are given a reprieve.
Disappointed boss Lee Ashforth said the club's fate was all-but sealed following their 2-1 defeat at Ossett earlier this month.
From that win, Ossett won three of their next four matches to pull clear - despite Railway also claiming wins over Prescot Cables and New Mills during that time.
Following the confirmation of the club's relegation, Ashforth said: "I stand by that I think the squad was good enough but the league table doesn't lie.
Forty-two was always the target and we are a little bit off that with three games to go. Because of that we have put ourselves in trouble.
"Losing to Ossett a couple of weeks ago was the turning point. It kicked them on and gave them a lift."
Chairman Nigel Corner said: "Last season after our most successful league campaign ever, I received quite a lot of praise, wrongly in my opinion, for the small part I played in that season.
"By the same token I take full responsibility for the failings of this season. As acting chairman the buck stops with me. I can only apologise I am truly sorry to my colleagues at the club and to the fans.
"This season has been a disappointment, nobody can question that, but we will survive and we will compete again next season."
It is the second time in five years that Railway have finished in the bottom two of the Evo-Stik First Division North.
In the 2011/12 season, Railway were given a reprieve to stay in the division following a miserable campaign under Nigel Danby,