Nelson became founder members of the new North West Counties Football League, joining the Third Division. They finished 10th (out of 18) in their first season, 1982–83. The 1986–87 season saw a 4th-placed finish. The following season the Third Division was scrapped, and Nelson were moved up to the Second Division, finishing in 16th. However, due to the poor state of their Victoria Park stadium, and problems with getting it up to the standard required by the league, the club were forced to drop down to the West Lancashire League, where they played in the Second Division and remained for four seasons from 1988–89 to 1991–92. They struggled though with a highest place finish of 15th. They were re-admitted to the North West Counties Second Division for the 1992–93 season after Victoria Park was upgraded, although they finished 17th (out of 18) in their first season. In 1996–97 they won the Division Two Trophy. In 1999–2000 they finished 3rd. In 2000–01 they finished in the third and final promotion place on the final day of the season above Atherton Laburnum Rovers. However, Atherton were granted a replay of their final game as their opponents had fielded an ineligible player. Atherton won the replayed game to snatch away third spot from Nelson. In 2005–06 they again finished 3rd and were promoted to the First Division, the club's first promotion in 83 years.