Formed in 1949 by Jimmy Drinkwater, the club was initially named Stockton Heath Albion and competed in the Warrington and District League until 1953, when they moved to the Mid Cheshire League. Freddie Worrall became manager at the same time, and during a 13-year spell in charge, the club won the league in 1959–60 plus the League Cup in three consecutive seasons during the 1950s. During his thirteen years at the helm, Heath were one of the most feared sides in Cheshire football, winning a string of honours including the Mid Cheshire League Championship in 1959–60, the League Cup in 1953–54, 1954–55, 1955–56 and made several appearances in the Cheshire Amateur Cup Final. 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.
At the club's 1961 AGM, it was decided to change the name to Warrington Town. In 1978 the club were founder members of Division Two of the Cheshire County League. When it merged into the North West Counties Football League in 1982, the club were founder members of Division Three. They finished as runners-up in the first season, earning promotion to Division Two. In 1985–86 Warrington reached the semi-finals of the FA Vase, losing 6–3 to Halesowen Town in a replay. After finishing as runners-up in Division Two in 1986–87, the club were promoted to Division One. In the same season they reached the FA Vase final, where they lost 3–2 to local rivals St Helens Town
In 1989–90 Warrington Town won Division One, and were promoted to the Northern Premier League. In 1992–93 they reached the quarter-finals of the FA Trophy, eventually losing 2–1 at Sutton United, and also became the first Division One club to reach the final of the League Cup, losing on penalties to Winsford United. The season also saw the club sell Neil Whalley to Football League Third Division side Preston North End for a £25,000, equalling the record fee paid for a Northern Premier League player. A few weeks later Warrington also sold Liam Watson to Preston for a record £60,000.
After finishing second bottom of the league in 1996–97, the club were relegated back to Division One of the North West Counties League. The following season they were demoted, failing ground grading. In the 1998–99 season, teenage striker Damien Whitehead set a new club record of 52 goals in just 42 appearances, before signing for Football League Division Three side Macclesfield Town at the end of the season. The 1999–2000 season saw Town win the Second Division Trophy beating Tetley Walker F.C (known as The Holden Final) 2–0 at Prescot Cables, with two goals from Neal Holden, whilst the following season saw Warrington win Division Two and earn promotion back to Division One. They finished fifth in 2003–04, and were promoted to Division One of the Northern Premier League as part of the restructuring that led to the creation of the Conference North and South. When Division One was split into northern and southern sections in 2007, the club were placed in the southern division, but were moved to the northern section the following season.
In 2014–15 the club reached the first round proper of the FA Cup for the first time in their history, where they beat League Two club Exeter City 1–0 with a 7th-minute header from defender and plasterer Craig Robinson, the brother of MK Dons manager Karl Robinson, in a giant-killing at Cantilever Park. The game was shown live on BBC Two. In the second round, Warrington Town lost 0–2 at Gateshead., televised live on BT Sport.
On 30 April 2015, the club lifted its first trophy in 14 years by defeating Farsley Celtic in the final of the Northern Premier League Challenge Cup (then called the Doodson Sport Cup) at Edgeley Park on penalties after the game finished scoreless.
The 2015–16 season began with Warrington Town aiming for promotion to the Northern Premier League Premier Division for the first time in the club's history. During the season the club set many new club records including scoring over 100 league goals and also winning over 30 league games in one season. Attendances at the club increased with a seasons average of 418 per game, including two crowds of over 1,000 for the games against Northwich Victoria and Prescot Cables
There was to be no repeat of the previous seasons FA Cup run as Town exited at the first hurdle in late August losing to Abbey Hey F.C.
After a relatively poor start to the season, with a win, a loss and 2 draws plus the FA Cup exit, Town embarked on an unbeaten run in the league of 9 wins and a draw from end August to mid October. During this unbeaten run, manager Shaun Reid was absent through illness for much of September, with Stuart Mellish, Lee Smith and the rest of the coaching staff standing in.
In the FA Trophy, Town won through 2 rounds before losing to AFC Fylde in November. The defence of the NPL Challenge Cup lasted just one match as they lost to Ramsbottom in a 3-times postponed match in early December.
There was another impressive unbeaten run in the league of 15 wins and a draw from late October until the first week of March, including separate runs of 5 and 6 clean sheets.
On 11 February, the club parted company with manager Shaun Reid by mutual consent. The Club decided not to renew his contract at the end of the season and the board agreed to his request to be released from his contract immediately. Stuart Mellish & Lee Smith took over as the management team until the end of the season.
This did not seem to affect the club's bid for promotion as Town lost only 2 more league games in the season, winning the other 12 games.
Needing just one point from the last 3 games of the season, Town won 6-1 at home against Prescot Cables in front of over 1400 spectators to seal the Championship title with 2 games remaining.
The final league record was 34 wins, 4 draws and just 4 defeats. Town won Division One North by 15 points setting division records of 106 points and 121 goals scored, beating the records set in the 2012-13 season. Town also scored in every one of the 42 league games.
Striker & Town captain Ciaran Kilheeney was the top scorer in all 3 NPL divisions with 37 league goals (the next highest was 29 goals). (He also scored 4 cup goals during the season.)
The team had an inconsistent start to the season. We exited the FA Cup in the first game. Also, several league games were lost to teams near the bottom of the table while beating Blyth Spartans and Buxton who were in the top 4.
After 16 games (with a record of W8, D1, L7) while 6th in the table & immediately following a home defeat by Workington, on 15-Oct-2016 the Club parted company with their management duo of Stuart Mellish and Lee Smith "by mutual consent". Reserve team coach Steve Hayes & Andy McCann stepped in as caretakers the day before a creditable away draw at Rushall Olympic
A week later the club appointed Paul Carden straight from his interim position at Tranmere Rovers along with club FA Cup talisman Craig Robinson and Mark Beesley