| Tue 23/08/16 | Stockport Town v Prestwich Heys | 3-1 | |  | | |
| Sat 27/08/16 | Stockport Town v Whitchurch Alport | 1-5 | | | | |
| Wed 31/08/16 | Litherland REMYCA v Stockport Town | 5-3 | | | | |
| Sat 03/09/16 | Stockport Town v AFC Blackpool | 3-1 | | | | |
| Sat 10/09/16 | Stockport Town v Holker Old Boys | 2-2 | | | | |
| Sat 17/09/16 | Stockport Town v Eccleshall | 7-1 | | | | |
| Tue 20/09/16 | Stockport Town v FC Oswestry Town | 2-3 | | | | |
| Sat 24/09/16 | Alsager Town v Stockport Town | 0-3 | | | | |
| Tue 27/09/16 | Stockport Town v Litherland REMYCA | 4-0 | | | | |
| Sat 01/10/16 | Sandbach United v Stockport Town | 4-2 | | | | |
| Sat 08/10/16 | Eccleshall v Stockport Town | 1-7 | | | | |
| Tue 11/10/16 | Chadderton v Stockport Town | 2-3 | | | |  |
| Sat 15/10/16 | Stockport Town v Alsager Town | 3-2 | | | | |
| Mon 17/10/16 | Daisy Hill v Stockport Town | 5-2 | | | | |
| Sat 22/10/16 | Stockport Town v Ryhope CW | 1-3 | | | | |
| Sat 29/10/16 | Carlisle City v Stockport Town | 2-2 | | | | |
| Sat 05/11/16 | Sandbach United v Stockport Town | 5-0 | | | | |
| Sat 12/11/16 | Stockport Town v Widnes | 2-3 | | | | |
| Sat 17/12/16 | Holker Old Boys v Stockport Town | 2-2 | | | | |
| Mon 26/12/16 | Cheadle Town v Stockport Town | 2-0 | | | | |
| Sat 07/01/17 | FC Oswestry Town v Stockport Town | 0-0 | | | | |
| Sat 14/01/17 | Stockport Town v Bacup Borough | 1-1 | | | | |
| Sat 21/01/17 | Charnock Richard v Stockport Town | 2-2 | | | | |
| Sat 28/01/17 | Stockport Town v Silsden | 2-1 | | | | |
| Sat 04/02/17 | Widnes v Stockport Town | 2-2 | | | | |
| Sat 11/02/17 | Stockport Town v Ashton Town | 7-0 | | | | |
| Sat 18/02/17 | Stockport Town v Charnock Richard | 1-0 | | | | |
| Sat 25/02/17 | Stockport Town v Sandbach United | 2-1 | | | | |
| Sat 11/03/17 | AFC Blackpool v Stockport Town | 2-2 | | | | |
| Thu 16/03/17 | St Helens Town v Stockport Town | 2-0 | | | | |
| Sat 01/04/17 | Bacup Borough v Stockport Town | 2-1 | | | | |
| Tue 04/04/17 | Atherton LR v Stockport Town | 0-2 | | | | |
| Fri 14/04/17 | Stockport Town v Cheadle Town | 1-5 | | | | |
| Sun 16/04/17 | Ashton Town v Stockport Town | 0-2 | | | | |
