| 1 | Tue 13 Dec 2016 | 161-5 v Forfar AthleticForfar Athletic 5-1 Annan Athletic | Ladbrokes League Two |
| 2 | Sat 17 Dec 2016 | 111-3 v Stirling AlbionStirling Albion 3-1 Annan Athletic | Ladbrokes League Two |
| 3 | Sat 24 Dec 2016 | 83-1 v Berwick RangersAnnan Athletic 3-1 Berwick Rangers | Ladbrokes League Two |
| 4 | Sat 31 Dec 2016 | 83-2 v ClydeClyde 2-3 Annan Athletic | Ladbrokes League Two |
| 5 | Sat 11 Feb 2017 | 1-0 v Edinburgh CityAnnan Athletic 1-0 Edinburgh City | Ladbrokes League Two |
| 6 | Sat 18 Feb 2017 | 1-0 v CowdenbeathCowdenbeath 0-1 Annan Athletic | Ladbrokes League Two |
| 7 | Sat 25 Feb 2017 | 1-0 v ClydeAnnan Athletic 1-0 Clyde | Ladbrokes League Two |
| 8 | Sat 11 Mar 2017 | 1-0 v Elgin CityAnnan Athletic 1-0 Elgin City | Ladbrokes League Two |
| 9 | Sat 18 Mar 2017 | 0-1 v Stirling AlbionStirling Albion 1-0 Annan Athletic | Ladbrokes League Two |
| 10 | Sat 25 Mar 2017 | 1-0 v CowdenbeathAnnan Athletic 1-0 Cowdenbeath | Ladbrokes League Two |
| 11 | Sat 1 Apr 2017 | 2-5 v ArbroathAnnan Athletic 2-5 Arbroath | Ladbrokes League Two |
| 12 | Sat 8 Apr 2017 | 1-2 v ClydeClyde 2-1 Annan Athletic | Ladbrokes League Two |
| 13 | Sat 15 Apr 2017 | 2-1 v Berwick RangersAnnan Athletic 2-1 Berwick Rangers | Ladbrokes League Two |
| 14 | Sat 22 Apr 2017 | 0-2 v Edinburgh CityEdinburgh City 2-0 Annan Athletic | Ladbrokes League Two |
| 15 | Sat 29 Apr 2017 | 5-1 v MontroseAnnan Athletic 5-1 Montrose | Ladbrokes League Two |
| 16 | Wed 10 May 2017 | 2-2 v Forfar AthleticAnnan Athletic 2-2 Forfar Athletic | Ladbrokes League Two Play-off |
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