Several players from this successful period went on to join Football League clubs, including Ian Weir, John Green, Alan Foster and Roger Hunt, later a World Cup winner with England in 1966.

The 1999–2000 season saw Town win the Second Division Trophy beating Tetley Walker 2–0 at Prescot Cables, with two goals from Neal Holden.

[1] In 2013–14 the club finished third in Division One North, qualifying for the promotion play-offs, where, they lost 1–0 at home to Bamber Bridge in the semi-finals.

Later in the season the club lifted its first trophy in 14 years by defeating Farsley Celtic on penalties in the final of the Northern Premier League Challenge Cup, held at Edgeley Park.

The Club Chairman decided to part company with manager Shaun Reid by mutual consent in February 2016, replacing him with Stuart Mellish and Lee Smith.

After 16 games of the 2016–17 season, while sixth in the table, management duo of Stuart Mellish and Lee Smith left by mutual consent and Chairman Macornac brought in Paul Carden.

They followed this up in 2018–19 with another third-placed finish, in a season made more complicated by the expulsion of North Ferriby United who went out of business partway through the campaign.

In the play-offs Warrington beat Nantwich Town 4–1 in a home semi-final, and then won 2–1 against South Shields in the final.

However, as a one-off for the 2018–19 season, Town had to play a "super playoff" game against the play-off winners of the newly-formed Southern League Premier Central Division.

After another abandoned season in 2020–21 and a play-off final defeat in 2021–22, it took more investment from the chairman which ensured Warrington finished the 2022–23 season as runners-up and were promoted to the National League North for the first time in club history, beating Bamber Bridge 1–0 in the play-off final at Cantilever Park.