McCall released 13 players at the end of the season,[3] and also lost his captain, David Wetherall, who decided to retire,[4] and Luke Medley, who turned down a new contract in favour of a return to his home in London.

[5] McCall added four new signings: keeper Jonathan McLaughlin,[6] midfielder Chris Brandon,[7] Paul Arnison and defender Graeme Lee during June as he attempted to build a team to win promotion.

[8][9] City returned to pre-season training on 1 July 2008 with a fifth new player, after Tranmere midfielder Paul McLaren signed a two-year deal.

[12] City's third friendly was a 2–1 defeat by another West Yorkshire non-league side, Guiseley, who featured former Bradford player David Brown on trial.

[19] The final pre-season friendly was played behind closed doors, when City lost 2–0 to Sheffield Wednesday with a team made up of juniors and reserve players.

[21] City again lost at the first round stage of the League Cup for the third successive season, this time 4–0 to West Yorkshire rivals Huddersfield Town.

[22] Thorne, who had been rested to the substitutes' bench for the defeat at Huddersfield, returned for City's second league game when he scored both goals in a 2–0 victory at Macclesfield Town.

[26] McCall stated he wanted to sign one more player before the August transfer deadline, before bringing in South African midfielder Dean Furman from his former side Rangers on loan until January.

[38] After recording just one victory in six matches, McCall said he wanted to bring in some loan transfers and signed Tom Clarke from Huddersfield on 23 October.

City were leading 1–0 at the time through an Omar Daley, and, despite being reduced to ten men, extended their advantage through former Grimsby striker Michael Boulding and a first club goal for Graeme Lee, eventually winning 3–1.

[40] Colbeck was injured during the victory over Grimsby, and so McCall signed midfielder Nicky Law, who had played ten games for City the previous season, as cover on another loan deal.

[43] The first round of the FA Cup saw City drawn against Milton Keynes Dons, who had won promotion to League One the previous season.

[59] City kept their fourth successive clean sheet the following day in the first game of 2009, but were again involved in a goalless draw, this time with fellow promotion-chasing side Shrewsbury Town.

[67] Two days after the game, City again moved into the loan market by taking Pakistani international defender Zesh Rehman for the rest of the season from Championship side QPR.

[68] Leaving the club on loan was another central defender, Mark Bower, who was signed by Luton Town for one month to cover injuries and suspensions.

[70][71] However, City made amends in their final game of the month by recording their first victory of the calendar year, 2–0 against a Grimsby side which had been reduced to ten men.

[72] The January transfer window closed two days later than traditionally, with City extending Jones' loan until the end of the season but deciding to allow O'Grady to return to Oldham.

[82] When City returned to the road three days later, they recorded a third consecutive away defeat, this time 3–0 to fellow promotion-contenders Rochdale, with all three goals coming in the second half.

[83] The following day, Northern Ireland international winger Keith Gillespie joined City for the rest of the season after he impressed Stuart McCall during two weeks training with the club.

[84] After another defeat, the fourth successive away from home, this time 1–0 to another side chasing promotion, Exeter City, Bradford once again dropped out of the play-off places.

[86] When City suffered their fifth successive away defeat, this time 4–1 to Bournemouth, only three days later,[87] Stuart McCall threatened to resign if the side missed out on a play-off place.

[90] McCall opted not to bring in any more new players by the transfer deadline,[91] but defender Simon Ainge was allowed to move on loan to Cambridge United.