| 1 | Sat 6 Aug 2016 | 40-3 v Dagenham & RedbridgeDagenham & Redbridge 3-0 Southport | National League |
| 2 | Tue 9 Aug 2016 | 40-3 v GatesheadSouthport 0-3 Gateshead | National League |
| 3 | Sat 13 Aug 2016 | 42-1 v WokingSouthport 2-1 Woking | National League |
| 4 | Sat 27 Aug 2016 | 41-1 v Tranmere RoversSouthport 1-1 Tranmere Rovers | National League |
| 5 | Mon 29 Aug 2016 | 41-5 v Forest Green RoversForest Green Rovers 5-1 Southport | National League |
| 6 | Sat 10 Sep 2016 | 41-1 v EastleighEastleigh 1-1 Southport | National League |
| 7 | Tue 13 Sep 2016 | 41-4 v BarrowSouthport 1-4 Barrow | National League |
| 8 | Sat 17 Sep 2016 | 41-1 v Aldershot TownSouthport 1-1 Aldershot Town | National League |
| 9 | Sat 24 Sep 2016 | 41-0 v North Ferriby UnitedNorth Ferriby United 0-1 Southport | National League |
| 10 | Sat 1 Oct 2016 | 41-2 v BromleySouthport 1-2 Bromley | National League |
| 11 | Sat 22 Oct 2016 | 41-1 v Sutton UnitedSouthport 1-1 Sutton United | National League |
| 12 | Tue 25 Oct 2016 | 42-0 v York CitySouthport 2-0 York City | National League |
| 13 | Sat 29 Oct 2016 | 42-1 v Torquay UnitedTorquay United 1-2 Southport | National League |
| 14 | Mon 7 Nov 2016 | 40-0 v Fleetwood TownSouthport 0-0 Fleetwood Town | Emirates FA Cup First Round |
| 15 | Sat 12 Nov 2016 | 43-2 v Maidstone UnitedSouthport 3-2 Maidstone United | National League |
| 16 | Tue 15 Nov 2016 | 41-4 v Fleetwood TownFleetwood Town 4-1 Southport | Emirates FA Cup First Round |
| 17 | Sat 19 Nov 2016 | 40-2 v Boreham WoodBoreham Wood 2-0 Southport | National League |
| 18 | Tue 22 Nov 2016 | 42-2 v ChesterChester 2-2 Southport | National League |
| 19 | Sat 26 Nov 2016 | 44-5 v Braintree TownSouthport 4-5 Braintree Town | National League |
| 20 | Tue 29 Nov 2016 | 40-0 v Solihull MoorsSouthport 0-0 Solihull Moors | National League |
| 21 | Sat 17 Dec 2016 | 44-3 v EastleighSouthport 4-3 Eastleigh | National League |
| 22 | Mon 26 Dec 2016 | 40-1 v WrexhamWrexham 1-0 Southport | National League |
| 23 | Sun 1 Jan 2017 | 43-2 v WrexhamSouthport 3-2 Wrexham | National League |
| 24 | Sat 7 Jan 2017 | 41-2 v Aldershot TownAldershot Town 2-1 Southport | National League |
| 25 | Tue 10 Jan 2017 | 41-0 v BarrowBarrow 0-1 Southport | National League |
| 26 | Sat 21 Jan 2017 | 42-4 v North Ferriby UnitedSouthport 2-4 North Ferriby United | National League |
| 27 | Sat 28 Jan 2017 | 41-3 v BromleyBromley 3-1 Southport | National League |
| 28 | Sat 4 Feb 2017 | 40-3 v GatesheadGateshead 3-0 Southport | National League |
| 29 | Sat 11 Feb 2017 | 41-4 v Dagenham & RedbridgeSouthport 1-4 Dagenham & Redbridge | National League |
| 30 | Sat 18 Feb 2017 | 40-0 v WokingWoking 0-0 Southport | National League |
| 31 | Sat 25 Feb 2017 | 40-1 v ChesterSouthport 0-1 Chester | National League |
| 32 | Sat 4 Mar 2017 | 42-4 v Maidstone UnitedMaidstone United 4-2 Southport | National League |
| 33 | Sat 18 Mar 2017 | 40-2 v Braintree TownBraintree Town 2-0 Southport | National League |
| 34 | Tue 21 Mar 2017 | 43-5 v York CityYork City 5-3 Southport | National League |
| 35 | Sat 25 Mar 2017 | 41-0 v Boreham WoodSouthport 1-0 Boreham Wood | National League |
| 36 | Sat 1 Apr 2017 | 40-1 v GuiseleySouthport 0-1 Guiseley | National League |
| 37 | Tue 4 Apr 2017 | 41-2 v Macclesfield TownSouthport 1-2 Macclesfield Town | National League |
| 38 | Sat 8 Apr 2017 | 42-2 v Sutton UnitedSutton United 2-2 Southport | National League |
| 39 | Fri 14 Apr 2017 | 40-3 v Dover AthleticDover Athletic 3-0 Southport | National League |
| 40 | Mon 17 Apr 2017 | 42-0 v Forest Green RoversSouthport 2-0 Forest Green Rovers | National League |
| 41 | Sat 22 Apr 2017 | 41-4 v Tranmere RoversTranmere Rovers 4-1 Southport | National League |
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