[11] Source:[12] 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.
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.
Curzon Ashton was reinstated to play Matlock Town in place of Witton Albion in the semi-finals.
[15] Source:[16] The Challenge Cup Final was played at the Throstle Nest, the home ground of Farsley F.C.
[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.