This re-election system was replaced by automatic promotion from 1987 onwards, but it came too late to help Runcorn who by then were no longer a top team in the Football Conference.

In 2000, they sold the Canal Street ground where they had played since 1918, and moved to the 11,000-seat Halton Stadium in Widnes, which was also used by the town's rugby team and Everton reserves.

During this season, the club's precarious financial state caused them to move out of the Halton Stadium permanently, having finished the previous season at Southport's Haig Avenue, and to share Valerie Park, home of local rivals Prescot Cables, who also played in the Northern Premier League.

After a second successive relegation, the club's future was in doubt, and the decision was made to officially confirm its resignation from the league and cease activity.

By this time, disgruntled supporters had already formed the breakaway club Runcorn Linnets F.C., which was granted membership of the North West Counties League Division Two for the 2006–07 season.