Due to Step Three leagues increasing their number of teams from 22 to 24 from the 2013–14 season onwards, only two teams will be relegated from the Premier Division, and only one team will be relegated from each of Division One North and South this season.[2]
Updated to match(es) played on 4 May 2013. Source: [1] Rules for classification: 1) points; 2) goal difference; 3) number of goals scored. (C) Champions; (P) Promoted; (R) Relegated Notes:
^Marine were deducted 3 points for fielding an ineligible player
Updated to match(es) played on 1 May 2013. Source: [2] Rules for classification: 1) points; 2) goal difference; 3) number of goals scored. (C) Champions; (P) Promoted; (R) Relegated Notes:
^Lancaster City deducted 3 points for fielding an ineligible player.
Updated to match(es) played on 4 May 2013. Source: [3] Rules for classification: 1) points; 2) goal difference; 3) number of goals scored. (C) Champions; (P) Promoted; (R) Relegated
The four clubs which make it through the preliminary round enter into the draw with the rest of the teams from the two Division One leagues which weren't drawn into the preliminary round.[8]
Teams from the Northern Premier League Premier Division entered at this stage, along with the 10 winners from the second round. The draw for the third round was made on 19 December 2012.[10]
The eight clubs to have made it through the fourth round were entered into the quarter-finals draw, which took place on 19 February 2013.[13]Cammell Laird, Farsley, and Curzon Ashton from the NPL Division One North and Northwich Victoria from the NPL Division One South remain as the lowest-placed teams still in the Cup.
The four clubs to have made it through the quarter-finals were entered into the semi-finals draw. The draw for the semi-finals took place on 21 March 2013, with Cammell Laird from the Northern Premier League Division One North remaining as the lowest-placed team still in the Cup.[14]Witton Albion was removed from the semi-finals due to fielding an ineligible player on 19 February 2013 against F.C. United of Manchester since the player had already represented Curzon Ashton in a previous round on 27 November 2012. Curzon Ashton was reinstated to play Matlock Town in place of Witton Albion in the semi-finals.[15]
The Challenge Cup Final was played at the Throstle Nest, the home ground of Farsley F.C.[17] This was the second consecutive Challenge Cup Final for North Ferriby United and Curzon Ashton's first Finals appearance. After a 1–1 draw, North Ferriby United went on to win the penalty shoot-out and secure their second Challenge Cup in a row while also being the third team ever to retain the Cup.[18]
For the 2013 edition of the Peter Swales Shield, the 2012–13 champions of the Northern Premier League First Division North, Skelmersdale United, played against the 2012–13 champions of the Northern Premier League First Division South, King's Lynn Town.