Eight days beforehand, York won their first national knockout competition, with a 2–0 victory over Newport County at Wembley Stadium in the 2012 FA Trophy Final.

Goalkeeper Michael Ingham, defender James Meredith and midfielder Paddy McLaughlin missed only three of the 58 competitive matches played over the season.

[5] Released following the end of the season were Neil Barrett, Chris Carruthers, Leon Constantine, Liam Darville, Michael Gash, Levi Mackin and Andy McWilliams.

[8][9][10][11][12] Jamal Fyfield,[13] Michael Ingham[14] and James Meredith signed new contracts with York,[15] with David McDermott being retained on non-contract terms.

[16] New additions in defence ahead of the season's start included goalkeeper Paul Musselwhite from Lincoln City[17] and defender Lanre Oyebanjo from Histon.

[18] Midfielders to sign were Paddy McLaughlin from Newcastle United,[19] Adriano Moke from Jerez Industrial (via the Glenn Hoddle Academy),[20] and Michael Potts from Blackburn Rovers,[21] with winger Matty Blair joining from Kidderminster Harriers.

[22] Strikers Ashley Chambers, who had been on loan the previous season, and Liam Henderson signed from Championship clubs Leicester City and Watford respectively.

[26] Walker scored an 83rd-minute penalty kick and a 90th-minute header to give York a 2–1 victory away to Ebbsfleet United in the opening match of the season.

[38][39] The team's first defeat of the season came after going down 1–0 at home to AFC Telford United, after former York striker Craig Farrell scored an 87th-minute goal.

[44] A second successive defeat at home came after losing 1–0 to Alfreton Town, with former York player Levi Mackin scoring the only goal with a penalty.

[58] A second match with Wrexham in eight days finished in a 0–0 draw at home, with Ingham making a number of fine saves to preserve the clean sheet.

[65] York were held to a 0–0 draw away to Telford, in which Boucaud, Blair and Walker were denied from scoring by opposition goalkeeper Ryan Young during the first 15 minutes.

[66] Challinor scored during stoppage time to secure an FA Trophy first round replay with Conference North team Solihull Moors, with the match ending a 2–2 draw at home.

[67][73] Challinor signed an extended contract until the end of the season, while McDermott was allowed to join Telford after being unable to break into the team.

[78] York won their FA Trophy second round match away to Salisbury City 6–2, with Blair, Reed, McLaughlin and Blinkhorn scoring the goals.

[82] Transfer deadline day saw the departure of Boucaud to Luton for a fee of £25,000,[83] while midfielder Erik Tønne was signed on loan from Sheffield United until the end of the season.

[87] Reed and Blinkhorn scored late goals to give York a 2–1 victory at home to Stockport, with the visitors having taken the lead earlier in the second half.

[89] Progression to the semi-final of the FA Trophy for the third time in five seasons came after York defeated Grimsby 1–0 away in the quarter-final, in which Scott Kerr scored his first goal for the club.

[94] York reached the FA Trophy final for the second time in four seasons after drawing 1–1 away to Luton in the semi-final second leg, with Blair scoring a 90th-minute equaliser, meaning the team went through 2–1 on aggregate.

[99] McLaughlin's third goal in three matches came in a 2–1 defeat away to Newport County, with the home team scoring the winner 20 minutes from time through Romone Rose.

[108] The result meant York finished fourth in the Conference Premier table and that they would play third-placed Mansfield in the play-off semi-final.

[111][112] The club won its first national knockout competition, and first piece of silverware in 19 years, after Newport were defeated 2–0 in the 2012 FA Trophy Final at Wembley Stadium, with Blair and Oyebanjo scoring in the second half.

[119] Prior to the club's Football League return, York released Ashikodi, Blinkhorn, Bopp and Brown,[120][121] while Meredith, Moke and Pilkington left on their own accord for Bradford City, Cambridge and Kidderminster.

[129] New players to join were defender Danny Blanchett from Burton Albion,[121] midfielders Lee Bullock from Bradford,[130] John McReady from Darlington[131] and Jonathan Smith from Swindon,[132] winger Michael Coulson from Grimsby,[133] and striker Oli Johnson from Oxford United.