| 1 | Sat 6 Aug 2016 | 40-1 v Elgin CityCowdenbeath 0-1 Elgin City | Ladbrokes League Two |
| 2 | Sat 13 Aug 2016 | 43-4 v Forfar AthleticForfar Athletic 4-3 Cowdenbeath | Ladbrokes League Two |
| 3 | Sat 20 Aug 2016 | 42-0 v Edinburgh CityCowdenbeath 2-0 Edinburgh City | Ladbrokes League Two |
| 4 | Sat 27 Aug 2016 | 43-5 v ClydeClyde 5-3 Cowdenbeath | Ladbrokes League Two |
| 5 | Sat 10 Sep 2016 | 42-1 v MontroseMontrose 1-2 Cowdenbeath | Ladbrokes League Two |
| 6 | Sat 17 Sep 2016 | 40-2 v Berwick RangersCowdenbeath 0-2 Berwick Rangers | Ladbrokes League Two |
| 7 | Sat 24 Sep 2016 | 40-0 v ArbroathArbroath 0-0 Cowdenbeath | Ladbrokes League Two |
| 8 | Sat 1 Oct 2016 | 40-2 v Stirling AlbionCowdenbeath 0-2 Stirling Albion | Ladbrokes League Two |
| 9 | Sat 15 Oct 2016 | 42-2 v Annan AthleticCowdenbeath 2-2 Annan Athletic | Ladbrokes League Two |
| 10 | Sat 29 Oct 2016 | 41-3 v Elgin CityElgin City 3-1 Cowdenbeath | Ladbrokes League Two |
| 11 | Sat 12 Nov 2016 | 42-0 v MontroseCowdenbeath 2-0 Montrose | Ladbrokes League Two |
| 12 | Sat 19 Nov 2016 | 41-1 v Edinburgh CityEdinburgh City 1-1 Cowdenbeath | Ladbrokes League Two |
| 13 | Sat 3 Dec 2016 | 41-0 v ClydeCowdenbeath 1-0 Clyde | Ladbrokes League Two |
| 14 | Sat 10 Dec 2016 | 40-2 v Annan AthleticAnnan Athletic 2-0 Cowdenbeath | Ladbrokes League Two |
| 15 | Sat 17 Dec 2016 | 43-4 v Forfar AthleticCowdenbeath 3-4 Forfar Athletic | Ladbrokes League Two |
| 16 | Sat 24 Dec 2016 | 40-2 v ArbroathCowdenbeath 0-2 Arbroath | Ladbrokes League Two |
| 17 | Sat 31 Dec 2016 | 42-1 v Stirling AlbionStirling Albion 1-2 Cowdenbeath | Ladbrokes League Two |
| 18 | Sat 18 Feb 2017 | 40-1 v Annan AthleticCowdenbeath 0-1 Annan Athletic | Ladbrokes League Two |
| 19 | Sat 25 Feb 2017 | 41-4 v ArbroathArbroath 4-1 Cowdenbeath | Ladbrokes League Two |
| 20 | Tue 28 Feb 2017 | 41-2 v Edinburgh CityCowdenbeath 1-2 Edinburgh City | Ladbrokes League Two |
| 21 | Sat 11 Mar 2017 | 43-1 v Berwick RangersBerwick Rangers 1-3 Cowdenbeath | Ladbrokes League Two |
| 22 | Sat 25 Mar 2017 | 40-1 v Annan AthleticAnnan Athletic 1-0 Cowdenbeath | Ladbrokes League Two |
| 23 | Sat 1 Apr 2017 | 41-0 v ClydeCowdenbeath 1-0 Clyde | Ladbrokes League Two |
| 24 | Sat 8 Apr 2017 | 41-1 v Edinburgh CityEdinburgh City 1-1 Cowdenbeath | Ladbrokes League Two |
| 25 | Sat 15 Apr 2017 | 43-0 v Stirling AlbionStirling Albion 0-3 Cowdenbeath | Ladbrokes League Two |
| 26 | Sat 22 Apr 2017 | 41-2 v ArbroathCowdenbeath 1-2 Arbroath | Ladbrokes League Two |
| 27 | Sat 29 Apr 2017 | 41-1 v Forfar AthleticCowdenbeath 1-1 Forfar Athletic | Ladbrokes League Two |
| 28 | Sat 6 May 2017 | 40-0 v Elgin CityElgin City 0-0 Cowdenbeath | Ladbrokes League Two |
| 29 | Sat 20 May 2017 | 41-1 v East KilbrideCowdenbeath 1-1 East Kilbride | Ladbrokes League Two Play-off Final |
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