They finished fifth in the table, and after beating Luton Town 2–0 on aggregate in the play-off semi-final, they lost 3–1 to Oxford United in the final at Wembley Stadium.

[3] The team finished the season in 17th-place in the Conference Premier table,[4] and were defeated 2–0 by Stevenage Borough in the 2009 FA Trophy Final at Wembley Stadium.

[6][7][8][9] Adam Boyes, Craig Farrell, Darren Kelly and Onome Sodje left for Scunthorpe United, Rushden & Diamonds, Portadown and Barnsley respectively.

[6][7][14] 11 players joined before the season kicked off; defenders James Meredith from Shrewsbury Town,[15] Alan O'Hare from Mansfield Town[16] and Djoumin Sangaré from Salisbury City,[17] midfielders Neil Barrett from Ebbsfleet United,[18] Andy Ferrell from Kidderminster Harriers,[14] Alex Lawless from Forest Green Rovers,[19] Levi Mackin from Wrexham,[15] winger Craig Nelthorpe from Oxford United,[14] and strikers Michael Gash from Ebbsfleet,[20] Richard Pacquette from Maidenhead United[15] and Michael Rankine from Rushden.

[50] Boyes rejoined the club on loan from Scunthorpe as cover for the injured Gash[51] ahead of a 1–1 home draw with Oxford, who equalised after York had taken the lead through Rankine.

[52] Barrett gave them the lead away to Luton Town, before the home team equalised through Asa Hall, the match finishing a 1–1 draw.

[53] York played Bedworth United in the FA Cup fourth qualifying round, and a 2–0 home win was secured with goals from Rankine and Brodie.

[60] Kevin Gall, a striker released by Darlington, was signed ahead of the match against Chester City,[61] which York won 3–2 after Brodie scored a hat-trick.

[70] Goals from Carruthers and Brodie gave York a 2–1 home win over Wrexham, a result that equalled the club record for successive victories in all competitions with eight.

[71] Youth-team defender Dean Lisles was promoted to the first-team squad, to provide cover for the injured Sangaré, O'Hare and Purkiss.

[72] York drew 0–0 away to Hinckley United in the first round of the FA Trophy,[73] and the replay at home was won 3–1, in which Brodie scored his second hat-trick of 2009–10.

[76] York were defeated 3–1 away by Premier League team Stoke City in the FA Cup third round, after they had taken the lead when Barrett scored a header from a Lawless free kick.

[82] York won their FA Trophy second round replay against Newport 1–0 at home, Pacquette scoring the winning goal in stoppage time.

[84] York beat Conference North team Corby Town 1–0 at home in the FA Trophy third round, the winning goal coming from a penalty scored by Ferrell.

[87][88] Purkiss gave York the lead away to Histon before Bradley Hudson-Odoi scored to equalise as the match finished a 1–1 draw, which ended a club record run of league victories at nine.

[97] York suffered a second straight league defeat after being beaten 2–1 away by Forest Green Rovers,[34] in which Mackin scored after his shot hit the back of an opposition player.

[98] Chester's expulsion from the Football Conference resulted in York having the three points gained against them from a 3–2 victory expunged, meaning the team moved down to sixth in the table.

[117] Following the match, the squad were forced to leave Kenilworth Road through the back of a stand after having missiles thrown at them by a section of Luton fans.

[118] The team lost the play-off final 3–1 to Oxford at Wembley, in which York scored from an own goal conceded by goalkeeper Ryan Clarke.

[120] York released Clarke, Gall, Mimms, Nelthorpe, O'Hare and Pacquette at the end of the season,[121] while Graham, Purkiss, Russell and Smith left for Kettering, Oxford, Cambridge and Mansfield respectively.

[126][127] York's summer signings were goalkeeper David Knight on a season-long loan from Histon,[128] defenders Duane Courtney from Kidderminster and Greg Young from Altrincham,[126] midfielder Jonathan Smith from Forest Green,[129] wingers David McDermott from Kidderminster[130] and Peter Till from and Walsall,[131] and striker George Purcell from Braintree Town.