Ahead of Colin Walker's first start to a season as manager, York signed nine players before the summer transfer window closed.

[7][8] Jimmy Beadle, Richard Brodie, Craig Farrell, Josh Mimms, Daniel Parslow, Ben Purkiss, Mark Robinson and Onome Sodje signed new contracts ahead of 2008–09.

[6][9] York signed seven players before the season started; they were goalkeepers Michael Ingham from Hereford United[10] and Artur Krysiak on a one-month loan from Birmingham City,[11] defender Mark Greaves from Burton Albion,[10] midfielders Niall Henderson from Raith Rovers,[12] Steven Hogg from Gretna and Ben Wilkinson from Hull City,[13] and striker Daniel McBreen from St Johnstone.

[14] Professional contracts were handed to three youth-team players, those being defenders Andy McWilliams and Josh Radcliffe and winger Liam Shepherd.

[31] Krysiak suffered a dislocated finger during this match, which resulted in him returning to Birmingham prematurely from his loan spell,[32] and was replaced by Mimms, who gave an assured performance.

[42] York drew for the fifth time in succession with a 1–1 home draw with Mansfield Town,[34] in which Sodje scored after he latched onto Adie Moses' misplaced header.

[45] Former Accrington Stanley striker David Brown, former Rotherham United defender Tom Hirst and Ipswich Town midfielder Jai Reason joined the club on trial.

[47] An 86th-minute equaliser from McBreen gave York a 1–1 draw at home to Salisbury City,[49] which maintained the team's unbeaten record at Bootham Crescent.

[52] Beadle was released by the club towards the end of his loan spell at Whitby, due to him looking for regular first-team football.

[56] Despite having the better chances, York drew 0–0 at home with Cambridge United,[57] before being beaten 3–1 away by Wrexham, in which Wilkinson scored a late consolation goal.

[58] The club made an attempt to re-sign former striker Clayton Donaldson on loan from Crewe Alexandra, but were told to make an inquiry four weeks later, due to him being injured.

[61] Walker revealed he was interested in signing striker Bruce Dyer, shortly after he played against York's reserve team for Bradford City.

[65] A 0–0 home draw with Mansfield in the fourth qualifying round of the FA Cup resulted in a replay, which would be played at Field Mill.

[70] Adam Boyes signed a long-term professional contract[71] ahead of York's Conference League Cup third round tie against Mansfield, which was won with a 4–2 penalty shoot-out victory.

[75] It was agreed that Brodie's loan at Barrow would be extended after he scored four goals in six appearances,[76] but York decided to overturn this decision a day later.

[78] He took charge of the team for the home match against Crawley, which finished a 2–2 draw after Lewis Killeen scored the rebound from a Thomas Pinault penalty in the 90th minute.

[81] Foyle made his first signing by bringing in winger Adam Smith on loan from Conference North club Gainsborough Trinity.

[89] York's two-match winning run ended after a 2–1 defeat away to league-leaders Burton Albion, which was secured after Greaves scored an own goal.

[91] Redfearn left the club to take charge of the Leeds under-18 team and Andy Porter, a former teammate of Foyle at Port Vale, was appointed as assistant manager.

[92] The New Year began with a second defeat of the season to Burton,[34] this time being beaten 3–1 at home, in which Brodie scored in the first half with a shot from the edge of the penalty area.

[104] His return came as a substitute in York's 1–1 draw away to Altrincham, in which Brodie scored the equalising goal after Shaun Densmore put the home team in the lead.

[115] York beat Conference South team Havant & Waterlooville 2–0 at home in the fourth round of the FA Trophy to secure a place in the semi-final, with both goals scored by McBreen.

[117] York's first league victory in a month[34] was a 2–0 home win over Weymouth, who were forced to play a weakened team due to their financial situation, and Brodie scored headers in each half.

[119] The first leg of the FA Trophy semi-final tie against AFC Telford United ended in a 2–0 away win, with goals in each half from Rusk and Purkiss.

[134] Brodie gave York a 14th-minute lead, and after Cliff Akurang equalised for Weymouth late in the first half, Boyes scored the winning goal 13 minutes from time.

[136] York were defeated 2–0 by Stevenage in the 2009 FA Trophy Final at Wembley, who scored with second-half goals from Steve Morison and Lee Boylan.

[96][138] After the season ended, York released Greaves, Hogg, McBreen, Pejic, Radcliffe, Robinson, Rusk, Shepherd, Christian Smith and Wilkinson.

[139][140][147] Over the summer York signed defenders James Meredith from Shrewsbury Town,[148] Alan O'Hare from Mansfield[149] and Djoumin Sangaré from Salisbury,[150] midfielders Neil Barrett from Ebbsfleet,[151] Andy Ferrell from Kidderminster,[147] Alex Lawless from Forest Green,[152] Mackin from Wrexham,[148] winger Craig Nelthorpe from Oxford,[147] and strikers Michael Gash from Ebbsfleet,[153] Richard Pacquette from Maidenhead United[148] and Michael Rankine from Rushden.