| 1 | Sat 6 Aug 2016 | 43-2 v Stirling AlbionAnnan Athletic 3-2 Stirling Albion | Ladbrokes League Two |
| 2 | Sat 13 Aug 2016 | 40-2 v Berwick RangersBerwick Rangers 2-0 Annan Athletic | Ladbrokes League Two |
| 3 | Sat 20 Aug 2016 | 43-2 v ClydeAnnan Athletic 3-2 Clyde | Ladbrokes League Two |
| 4 | Sat 27 Aug 2016 | 42-2 v MontroseMontrose 2-2 Annan Athletic | Ladbrokes League Two |
| 5 | Sat 10 Sep 2016 | 41-2 v Forfar AthleticAnnan Athletic 1-2 Forfar Athletic | Ladbrokes League Two |
| 6 | Sat 17 Sep 2016 | 41-1 v ArbroathArbroath 1-1 Annan Athletic | Ladbrokes League Two |
| 7 | Sat 24 Sep 2016 | 41-1 v Edinburgh CityAnnan Athletic 1-1 Edinburgh City | Ladbrokes League Two |
| 8 | Sat 5 Nov 2016 | 181-2 v ArbroathAnnan Athletic 1-2 Arbroath | Ladbrokes League Two |
| 9 | Sat 12 Nov 2016 | 30-1 v Edinburgh CityEdinburgh City 1-0 Annan Athletic | Ladbrokes League Two |
| 10 | Sat 19 Nov 2016 | 151-0 v Elgin CityAnnan Athletic 1-0 Elgin City | Ladbrokes League Two |
| 11 | Sat 10 Dec 2016 | 142-0 v CowdenbeathAnnan Athletic 2-0 Cowdenbeath | Ladbrokes League Two |
| 12 | Sat 24 Dec 2016 | 173-1 v Berwick RangersAnnan Athletic 3-1 Berwick Rangers | Ladbrokes League Two |
| 13 | Sat 18 Feb 2017 | 1-0 v CowdenbeathCowdenbeath 0-1 Annan Athletic | Ladbrokes League Two |
| 14 | Sat 25 Feb 2017 | 1-0 v ClydeAnnan Athletic 1-0 Clyde | Ladbrokes League Two |
| 15 | Sat 11 Mar 2017 | 1-0 v Elgin CityAnnan Athletic 1-0 Elgin City | Ladbrokes League Two |
| 16 | Sat 18 Mar 2017 | 0-1 v Stirling AlbionStirling Albion 1-0 Annan Athletic | Ladbrokes League Two |
| 17 | Sat 25 Mar 2017 | 1-0 v CowdenbeathAnnan Athletic 1-0 Cowdenbeath | Ladbrokes League Two |
| 18 | Sat 1 Apr 2017 | 2-5 v ArbroathAnnan Athletic 2-5 Arbroath | Ladbrokes League Two |
| 19 | Sat 8 Apr 2017 | 1-2 v ClydeClyde 2-1 Annan Athletic | Ladbrokes League Two |
| 20 | Sat 15 Apr 2017 | 2-1 v Berwick RangersAnnan Athletic 2-1 Berwick Rangers | Ladbrokes League Two |
| 21 | Sat 22 Apr 2017 | 0-2 v Edinburgh CityEdinburgh City 2-0 Annan Athletic | Ladbrokes League Two |
| 22 | Sat 29 Apr 2017 | 5-1 v MontroseAnnan Athletic 5-1 Montrose | Ladbrokes League Two |
| 23 | Wed 10 May 2017 | 2-2 v Forfar AthleticAnnan Athletic 2-2 Forfar Athletic | Ladbrokes League Two Play-off |
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