In 1890/91 Chester joined the Combination League, and put in a strong performance in their first season, finishing third, while reaching the last 16 of the FA Cup, where they were eliminated by the eventual winners Blackburn Rovers.
At the end of the 1897–98 season Chester were forced to leave Faulkner Street due to buildings encroaching on the ground, and moved to land which had previously been used for the Royal Agricultural Show in 1893.
In 1908/9 Chester finally made the breakthrough of winning the Combination, losing only two games out of 30 in the season, and finishing eight points ahead of second placed Saltney.
However, following the outbreak of World War 1 attendances dropped considerably, and although the Lancashire Combination played out the season, Chester withdrew from the league in March, and their record was expunged.
After World War I, they became founder members of the Cheshire County League, which was substantially founded from clubs which had been part of the Lancashire Combination, including Witton Albion, Macclesfield, Northwich and Altrincham, providing Chester with more local derbies than previously.
The appointment, and the players whom Hewitt brought in, was an immediate success, with 170 goals scored in 42 league fixtures, with forward Arthur Gale netting 102 times in all competitions.
After a summer of excitement, Chester played their first Football League match against Wigan Borough in Division Three North on 29 August 1931 at Sealand Road in front of a gate of 12,770.
The 1933–34 season was the first since entering the League where Chester did not challenge for promotion, slipping to tenth in the table; indeed, the team needed to win eight of their last ten fixtures to finish that high, having been fifth from bottom after the 9–0 defeat at Barrow on 10 February.
The turnaround was sparked by the club making three signings on 15 March, of Arthur Wilson, Charlie Sargeant and John Wallbanks, a striker who scored 12 goals in the last ten matches.
Led by the goals of Wallbanks, Chester's good form continued into the 1934–35 season, and the club lay top of the table at the start of April.
However, following the transfer of Wallbanks to Bradford PA, one win in the last six matches was not enough to maintain the lead, and Chester finished the season in third place, missing out on promotion.
The Blues' consistent run of strong league positions continued in 1936–37 with a third-place finish, with the team also retaining the Division 3 North Cup.
1938–39 saw something of a resurgence, however, with the club ending the season in sixth place, and a long FA Cup run culminating in a fourth round exit to Sheffield Wednesday after two replays.
Ken Roberts had the honour of being the first Chester manager to win promotion in the Football League, although much credit went to inspirational coach Brian Green.
After beating Walsall, Blackpool and Bobby Charlton's Preston North End, Chester hosted Football League champions Leeds United in round four.
On an incredible night, two goals from John James and one from Trevor Storton gave Chester a 3–0 win that is regarded as one of the greatest shocks in the competition's history.
Three years later they narrowly missed out on a play-off spot as McNally worked miracles on a limited budget, but further bad times lay ahead.
Unfortunately, the shock resignation of manager Graham Barrow and the departure of several key players in the close-season of 1994 left Chester with a threadbare squad, and they were comfortably relegated back to Division Three in 1995.
Despite their off-field problems, Chester comfortably avoided relegation from the Third Division under Kevin Ratcliffe in 1998–99 and their appeared to be fresh hope when Terry Smith became new owner in July 1999.
After relegation from the League, Mark Atkins left the club, replaced by popular former manager Graham Barrow, while Luke Beckett moved to Chesterfield for a fee finally set by a tribunal at £175,000.
In the league, the first season in the Conference petered out into an eighth-place finish, with Chester earning 62 points from their 42 matches during a campaign where Rushden & Diamonds mostly looked uncatchable as leaders.
On 20 June, manager Graham Barrow was fired by Terry Smith in a phone conversation, and replaced by former Manchester United player Gordon Hill; in the meantime Paul Beesley was sacked for the second time in as many months.
Good form in the second half of the season under Wright both saw Chester reach the Sixth Round of the FA Trophy, and climb to 14th place in the final table and comfortably avoiding relegation to the Northern Premier League.
For much of the season, the lead in the table switched between Chester and Hereford United, but the title was finally secured with a 1–0 win at the Deva Stadium against Scarborough.
Mark Wright resigned the day before the season started, with Ray Mathias rapidly appointed to be in caretaker charge for Chester's 1–1 draw at Notts County.
By the end of August, Chester were bottom of the League but their fortunes improved under new manager, and ex-player, Ian Rush, who received his first managerial appointment.
However, Chester's financial difficulties once again reared their head, with the Inland Revenue filing a petition to wind up the club over a £180,000 debt, which was settled in September.
In a surprising turn of events, Mark Wright returned to the club which he had resigned from less than two years previously, and a run of five successive wins late in the season secured another campaign in the Football League.
The season began in disastrous style for the Blues, with a 6–0 defeat at Dagenham, and five goals conceded in the first 35 minutes of the League Cup tie against Leeds United.
The club's financial problems continued to mount, and a prohibition order was issued on the Deva Stadium after police withdrew their services after the non-payment of bills.