| Sat 02/08/25 | Chadderton v Stockport Town (CUP) * | 2-1 | | | | | | |
| Sat 09/08/25 | Stockport Town v Padiham * | 1-2 | | | | | | |
| Mon 11/08/25 | Stockport Town v Prestwich Heys * | 1-1 | | | | | | |
| Sat 16/08/25 | Stockport Town v Cheadle Town * | 2-1 | | | | | | |
| Sat 23/08/25 | Stockport Town v Selby Town (CUP) * | 3-0 | |  | | | | |
| Mon 25/08/25 | Atherton LR v Stockport Town * | 5-0 | | | | | | |
| Tue 23/09/25 | Barnoldswick Town v Stockport Town * | 3-3 | | | | | | |
| Sat 04/10/25 | Stockport Town v Irlam * | 0-3 | | | | | | |
| Tue 07/10/25 | Glossop North End v Stockport Town * | 1-2 |  | | | | | |
| Sat 11/10/25 | Wythenshawe v Stockport Town * | 2-1 | | | | | | |
| Mon 13/10/25 | Stockport Town v Hyde United (CUP) * | 4-1 | | | | | | |
| Mon 20/10/25 | Stockport Town v City of Liverpool * | 0-2 | | | | | | |
| Mon 03/11/25 | Stockport Town v Burscough * | 1-3 | | | | | | |
| Sat 08/11/25 | Stockport Town v Glossop North End * | 1-2 | | | | | | |
| Sat 15/11/25 | Stockport Town v Barnoldswick Town | 2-0 | | | | | | |
| Mon 17/11/25 | Stockport Town v Warrington Town (CUP) | 2-0 | | | | | | |
| Sat 22/11/25 | Litherland REMYCA v Stockport Town | 0-6 | | | | | | |
| Sat 29/11/25 | Stockport Town v Longridge Town | 1-2 | | | | | | |
| Wed 03/12/25 | West Didsbury & Chorlton v Stockport Town * | 1-3 | | | | | | |
| Sat 06/12/25 | Stockport Town v FC St Helens * | 0-4 | | | | | | |
| Sat 31/01/26 | Longridge Town v Stockport Town * | 1-2 | | | | | | |
| Tue 03/02/26 | Charnock Richard v Stockport Town * | 1-2 | | | | | | |
| Sat 07/02/26 | Stockport Town v Pilkington * | 4-0 | | | | | | |
| Tue 10/03/26 | Irlam v Stockport Town * | 0-0 | | | | | | |
