Hull City Association Football Club was founded in June 1904. For some years prior to this, attempts were made to found a football club, but in a city dominated initially by rugby league with teams such as Hull FC and Hull KR, who were both respectable teams, this proved difficult.

Hull City's first season as a professional football club consisted only of friendly matches, as due to the time of founding, Hull were unable to apply for membership to The Football League for the 1904–05 season. These early matches were played at The Boulevard, the old home of rugby league side Hull FC. On 1 September 1904, Hull's debut match took place against Notts County; with 6000 in attendance at The Boulevard, Hull notched up an impressive start, holding the more experienced County to a 2–2 draw.

Hull's first competitive football game was in the FA Cup, but they were eliminated, after a replay, in the preliminary round against Stockton, the score was 7–4 on aggregate. After disputes with landlords at The Boulevard, Hull City moved to Anlaby Road Cricket Ground. After having played 44 friendly fixtures the previous season, Hull City were finally entered into the Football League Second Division for the 1905–06 season. Other teams competing in the league that season included the likes of Manchester United and Chelsea, as well as Yorkshire rivals Leeds City, Bradford City and Barnsley. Hull faced Barnsley in their first game, a fixture which Hull won 4–1. Eventually, Hull would finish the season in fifth place.

The following season a new ground was built for Hull City across the road from the cricket ground. Still under the managership of Ambrose Langley, Hull continued to finish consistently in the top half of the table. They came agonisingly close to promotion in the 1909–10 season, recording what would be their highest ever finish in their history. Hull finished third, level on points with second placed Oldham Athletic, missing promotion on goal average by the slim margin of 0.29 of a goal.

Before World War I, Hull reached the quarter-finals of the FA Cup in 1915, beating West Bromwich Albion, Northampton Town and Southampton, before eventually going out to Bolton Wanderers in a 4–2 away defeat. In cup competitions, the club's greatest achievement was in 1930, when they reached the FA Cup semi-final. The cup run saw Hull knocking out Leeds United and eventual Champions of the Second and Third Division; Blackpool and Plymouth Argyle respectively. They then knocked out Manchester City, to meet Newcastle United in the FA Cup quarter finals. The first leg at St James' Park finished as a 1–1 draw, but in the replay Hull beat Newcastle 1–0. The semi-final match against Arsenal took place at Elland Road in Leeds, the game ended 2–2, and was taken to a replay. Arsenal knocked Hull out at Aston Villa's home ground, the game ended 1–0.

In the 1948–49 season, managed by former England international Raich Carter, Hull won the Third Division (North), and their newly built Boothferry Park ground saw a crowd approaching 50,000 for the Christmas Day game against Rotherham United, and exceeded by that for the FA Cup 6th round tie with Manchester United; the attendance of 55,019 still remains a record today.

'Yo-yoing' between the second and third tiers of English football, Hull City had promotion seasons from the Third to the Second Division again in 1959 and 1966, winning the Third Division in the latter season. Hull became the first team in the world to go out of a cup competition on penalties, which came against Manchester United in the semi-final of the Watney Mann Invitation Cup on 1 August 1970. By the early 1980s, Hull City were down in the Fourth Division, and financial collapse lead to receivership.

The low ebb saw the arrival of unlikely looking saviours in the form of a chairman (Don Robinson) and manager (Colin Appleton) from the footballing outpost of Scarborough F.C. Promotion to Division Three followed in 1983, with a young team featuring the likes of future England international Brian Marwood, future England manager Steve McClaren, fearsome centre-forward Billy Whitehurst, and the prolific goal-scorer Les Mutrie. When Hull City missed out on promotion by one goal the following season, Appleton left to manage Swansea City.

Hull reached the Second Division in 1985 under new player-manager Brian Horton. They defied the odds to stay there for the next five years before finally going down in 1991, by which time the club's manager was Terry Dolan. Hull finished 14th in the Third Division in the 1991–92 season, meaning that they would be competing in the new Football League Division Two the following season. In their first season in the rebranded division, Hull narrowly avoided another relegation but the board kept faith in Dolan and over the next two seasons they achieved secure mid table finishes. But terrible form in the 1995–96 season condemned Hull to relegation to Division Three.

The club was purchased by former tennis player David Lloyd in 1997 and sacked Dolan as manager, who was replaced with Mark Hateley as boss after Hull could only finish in 17th place in the table in the 1996–97 season. Hull's league form was steadily deteriorating to the point that relegation to the Conference was looking a real possibility. Lloyd sold the club in November 1998 to a South Yorkshire based consortium. Hateley departed in November 1998 to be replaced by 34-year-old veteran player Warren Joyce, who steered the club to safety after being anchored to the foot of the table. Hull City fans refer to this season as "The Great Escape". After this feat, Joyce was perhaps unlucky to be replaced in April 2000 by the experienced Brian Little.

Little breathed new life into Hull and managed to get good results out of the players, despite briefly being locked out of Boothferry Park by the bailiffs and with liquidation looking a real possibility. Hull qualified for the Division Three playoffs in the 2000–01 season, losing in the semi-finals. A boardroom takeover by former Leeds United commercial director Adam Pearson had eased the club's precarious financial situation and all fears of closure were banished.

The new chairman ploughed funds into the club, allowing Little to rebuild the team. Hull occupied the Division Three promotion and playoff places for much of the 2001–02 season, but Little was sacked two months before the end of the season and Hull slipped to 11th under his successor Jan Mølby.

Hull began the 2002–03 season with a terrible start, which saw relegation look more likely than promotion, and Mølby was sacked in October as Hull languished fifth from bottom in the league. Peter Taylor was named as Hull's new manager and in December 2002, just two months his appointment, Hull relocated to the impressive new 25,400-seater Kingston Communications Stadium after 56 years at Boothferry Park.

The two seasons which followed the opening of the new stadium were hugely successful. Hull were Division Three runners-up in 2003–04 and League One runners-up in 2004–05. These back-to-back promotions took them into the Championship, the second tier of English football. The 2005–06 season, the club's first back in the second tier, saw Hull finish in 18th place, a comfortable 10 points clear of relegation and their highest league finish for 16 years.

However, Taylor left the club on 13 June 2006 to take up the manager's job at Crystal Palace. Phil Parkinson was confirmed as his replacement on 29 June 2006, but was sacked on 4 December 2006 with Hull in the relegation zone, despite having spent over £2 million on players. Phil Brown took over as caretaker manager, and took over permanently in January 2007, having taken Hull out of the relegation zone. Brown brought veteran striker Dean Windass back to his hometown club on loan from Bradford City,and his eight goals helped secure Hull's Championship status as they finished in 21st place. At the end of the season, another familiar face, former manager Brian Horton, rejoined the club as Phil Brown's assistant.

Chairman Pearson sold the club to a consortium led by Paul Duffen in June 2007, stating that he "had taken the club as far as I could", and would have to relinquish control in order to attract "really significant finance into the club". He resigned from the board on 31 July 2007, thus severing all ties with the club.