By the turn of the year York were only above the relegation zone on goal difference, before a 17-match unbeaten run saw the team finish in seventh-place in the 24-team 2013–14 League Two.

[7] Following the previous season's conclusion Lee Bullock, Jon Challinor, Chris Doig, Ben Everson, Scott Kerr, David McDaid, Paddy McLaughlin, Michael Potts, Jamie Reed and Jason Walker were released by York,[8][9] while Matty Blair departed for Fleetwood Town.

[10] David McGurk, Lanre Oyebanjo, Daniel Parslow, Tom Platt and Chris Smith signed new contracts with the club.

[14] Defender Mike Atkinson and striker Chris Dickinson entered the first-team squad from the youth team after agreeing professional contracts.

[33][34] Jarvis gave York the lead away to Exeter City before Alan Gow scored in each half to see the home team win 2–1.

[35] York suffered their first home league defeat of the season after AFC Wimbledon won 2–0, with Michael Smith scoring in each half.

[40] York achieved their first win since the opening day of the season after beating Portsmouth 4–2 at home, with Fletcher (2), Montrose and Jarvis scoring.

[45] York drew 2–2 away to Chesterfield, having taken a two-goal lead through O'Neill and Jarvis, before the home team fought back through Armand Gnanduillet and Jay O'Shea.

[46] The team then hosted Fleetwood Town, and the visitors won 2–0 with goals scored in each half by Gareth Evans and Jamille Matt.

[47] Scunthorpe United were beaten 4–1 at home to end York's three-match run without a win, with all the team's goals coming in the first half from Carson, Fletcher and Brobbel (2).

[49] York drew 3–3 away to Bristol Rovers to earn a first round replay in the FA Cup, taking the lead through Jarvis before Eliot Richards equalised for the home team.

[55] Kevan Hurst gave Southend the lead early into the match and Bowman equalised for York with a low strike during the second half, before Luke Prosser scored the winning goal for the home team in stoppage time.

[62][63] York drew 0–0 at home with second-placed Oxford United, in which Carson came closest to scoring with a volley that flashed across the face of the goal.

[78] Defender John McCombe was signed on a two-and-a-half-year contract following his release from Mansfield,[79] before Clay and Jamal Fyfield left York by mutual consent.

[90] Having worn the armband since an injury to McGurk, Penn was appointed captain for the rest of the season, a position that had earlier been held by Smith and Parslow.

[98] He made his debut as a substitute in York's 1–0 home win over bottom of the table Torquay, in which Hayhurst scored the only goal in the 11th minute with an 18-yard shot that deflected off Aaron Downes.

[45] With the team recording six wins and one draw in March 2014, including six clean sheets, Worthington was named League Two Manager of the Month.

[101] Pope made a number of saves as York held league leaders Rochdale to a 0–0 away draw, with a point being enough to lift the team back into seventh-place.

[104] York consolidated their place in a play-off position after beating Bury 1–0 at home with a fifth-minute goal scored by Lowe from a Hayhurst corner.

[105] A place in the League Two play-offs was secured following a 1–0 win over Newport at home, in which Coulson scored the only goal in the 77th minute with a 25-yard free kick.

[108] This result meant York finished the season in seventh-place in League Two, and would thus play fourth-placed Fleetwood in the play-off semi-final on the back of a 17-match unbeaten run.

[114] After the season ended York released Tom Allan, Andrew, Dickinson, McDonald, Puri and Reed, while McGurk retired from professional football.

[118] York's summer signings included goalkeeper Jason Mooney from Tranmere Rovers,[119] defenders Femi Ilesanmi from Dagenham,[120] Marvin McCoy from Wycombe[121] and Dave Winfield from Shrewsbury Town,[122] midfielders Lindon Meikle from Mansfield,[123] Anthony Straker from Southend[124] and Luke Summerfield from Shrewsbury,[125] and striker Jake Hyde from Barnet.