| 1 | Sat 6 Aug 2016 | 30-2 v BlackpoolBlackpool 2-0 Exeter City | Sky Bet League Two |
| 2 | Sat 13 Aug 2016 | 31-2 v Hartlepool UnitedExeter City 1-2 Hartlepool United | Sky Bet League Two |
| 3 | Sat 20 Aug 2016 | 32-1 v Accrington StanleyAccrington Stanley 1-2 Exeter City | Sky Bet League Two |
| 4 | Tue 23 Aug 2016 | 31-3 v Hull CityExeter City 1-3 Hull City | EFL Cup Second Round |
| 5 | Sat 24 Sep 2016 | 32-0 v StevenageStevenage 0-2 Exeter City | Sky Bet League Two |
| 6 | Tue 27 Sep 2016 | 30-2 v Notts CountyExeter City 0-2 Notts County | Sky Bet League Two |
| 7 | Sat 1 Oct 2016 | 30-1 v Wycombe WanderersWycombe Wanderers 1-0 Exeter City | Sky Bet League Two |
| 8 | Sat 8 Oct 2016 | 30-0 v Grimsby TownExeter City 0-0 Grimsby Town | Sky Bet League Two |
| 9 | Sat 15 Oct 2016 | 34-1 v BarnetBarnet 1-4 Exeter City | Sky Bet League Two |
| 10 | Sat 22 Oct 2016 | 31-2 v Cambridge UnitedExeter City 1-2 Cambridge United | Sky Bet League Two |
| 11 | Sat 29 Oct 2016 | 33-0 v MorecambeMorecambe 0-3 Exeter City | Sky Bet League Two |
| 12 | Sat 5 Nov 2016 | 31-3 v Luton TownExeter City 1-3 Luton Town | Emirates FA Cup First Round |
| 13 | Tue 8 Nov 2016 | 31-1 v Swindon TownExeter City 1-1 Swindon Town | Checkatrade Trophy Southern Group C |
| 14 | Sat 12 Nov 2016 | 31-3 v Doncaster RoversExeter City 1-3 Doncaster Rovers | Sky Bet League Two |
| 15 | Sat 19 Nov 2016 | 32-3 v Carlisle UnitedCarlisle United 3-2 Exeter City | Sky Bet League Two |
| 16 | Tue 22 Nov 2016 | 31-0 v Leyton OrientLeyton Orient 0-1 Exeter City | Sky Bet League Two |
| 17 | Sat 26 Nov 2016 | 30-0 v Luton TownExeter City 0-0 Luton Town | Sky Bet League Two |
| 18 | Sat 10 Dec 2016 | 33-1 v Cheltenham TownCheltenham Town 1-3 Exeter City | Sky Bet League Two |
| 19 | Sat 17 Dec 2016 | 32-0 v Mansfield TownExeter City 2-0 Mansfield Town | Sky Bet League Two |
| 20 | Mon 26 Dec 2016 | 30-0 v Yeovil TownYeovil Town 0-0 Exeter City | Sky Bet League Two |
| 21 | Mon 2 Jan 2017 | 34-0 v Leyton OrientExeter City 4-0 Leyton Orient | Sky Bet League Two |
| 22 | Sat 14 Jan 2017 | 33-0 v Grimsby TownGrimsby Town 0-3 Exeter City | Sky Bet League Two |
| 23 | Sat 21 Jan 2017 | 33-0 v Colchester UnitedExeter City 3-0 Colchester United | Sky Bet League Two |
| 24 | Sat 28 Jan 2017 | 31-0 v PortsmouthPortsmouth 0-1 Exeter City | Sky Bet League Two |
| 25 | Tue 31 Jan 2017 | 34-2 v Wycombe WanderersExeter City 4-2 Wycombe Wanderers | Sky Bet League Two |
| 26 | Sat 4 Feb 2017 | 34-0 v Crewe AlexandraExeter City 4-0 Crewe Alexandra | Sky Bet League Two |
| 27 | Sat 11 Feb 2017 | 30-3 v Plymouth ArgylePlymouth Argyle 3-0 Exeter City | Sky Bet League Two |
| 28 | Tue 14 Feb 2017 | 32-2 v Notts CountyNotts County 2-2 Exeter City | Sky Bet League Two |
| 29 | Sat 18 Feb 2017 | 31-1 v StevenageExeter City 1-1 Stevenage | Sky Bet League Two |
| 30 | Sat 25 Feb 2017 | 32-2 v BlackpoolExeter City 2-2 Blackpool | Sky Bet League Two |
| 31 | Tue 28 Feb 2017 | 32-1 v Crawley TownCrawley Town 1-2 Exeter City | Sky Bet League Two |
| 32 | Sat 4 Mar 2017 | 31-3 v Hartlepool UnitedHartlepool United 3-1 Exeter City | Sky Bet League Two |
| 33 | Sat 11 Mar 2017 | 30-2 v Accrington StanleyExeter City 0-2 Accrington Stanley | Sky Bet League Two |
| 34 | Tue 14 Mar 2017 | 33-0 v Cheltenham TownExeter City 3-0 Cheltenham Town | Sky Bet League Two |
| 35 | Sat 18 Mar 2017 | 31-1 v Luton TownLuton Town 1-1 Exeter City | Sky Bet League Two |
| 36 | Sat 25 Mar 2017 | 33-3 v Yeovil TownExeter City 3-3 Yeovil Town | Sky Bet League Two |
| 37 | Sun 14 May 2017 | 33-3 v Carlisle UnitedCarlisle United 3-3 Exeter City | Sky Bet League Two Play-off |
| 38 | Thu 18 May 2017 | 33-2 v Carlisle UnitedExeter City 3-2 Carlisle United | Sky Bet League Two Play-off |
| 39 | Sun 28 May 2017 | 31-2 v BlackpoolBlackpool 2-1 Exeter City | Sky Bet League Two Play-off |
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