| 1 | Sat 6 Aug 2016 | 50-3 v Dagenham & RedbridgeDagenham & Redbridge 3-0 Southport | National League |
| 2 | Tue 9 Aug 2016 | 50-3 v GatesheadSouthport 0-3 Gateshead | National League |
| 3 | Sat 13 Aug 2016 | 52-1 v WokingSouthport 2-1 Woking | National League |
| 4 | Tue 16 Aug 2016 | 51-3 v Macclesfield TownMacclesfield Town 3-1 Southport | National League |
| 5 | Sat 20 Aug 2016 | 50-4 v Lincoln CityLincoln City 4-0 Southport | National League |
| 6 | Sat 27 Aug 2016 | 51-1 v Tranmere RoversSouthport 1-1 Tranmere Rovers | National League |
| 7 | Mon 29 Aug 2016 | 51-5 v Forest Green RoversForest Green Rovers 5-1 Southport | National League |
| 8 | Sat 3 Sep 2016 | 50-1 v Dover AthleticSouthport 0-1 Dover Athletic | National League |
| 9 | Sat 10 Sep 2016 | 51-1 v EastleighEastleigh 1-1 Southport | National League |
| 10 | Sat 17 Sep 2016 | 51-1 v Aldershot TownSouthport 1-1 Aldershot Town | National League |
| 11 | Sat 8 Oct 2016 | 51-2 v GuiseleyGuiseley 2-1 Southport | National League |
| 12 | Sat 22 Oct 2016 | 51-1 v Sutton UnitedSouthport 1-1 Sutton United | National League |
| 13 | Tue 25 Oct 2016 | 52-0 v York CitySouthport 2-0 York City | National League |
| 14 | Sat 29 Oct 2016 | 52-1 v Torquay UnitedTorquay United 1-2 Southport | National League |
| 15 | Mon 7 Nov 2016 | 50-0 v Fleetwood TownSouthport 0-0 Fleetwood Town | Emirates FA Cup First Round |
| 16 | Sat 12 Nov 2016 | 53-2 v Maidstone UnitedSouthport 3-2 Maidstone United | National League |
| 17 | Tue 15 Nov 2016 | 51-4 v Fleetwood TownFleetwood Town 4-1 Southport | Emirates FA Cup First Round |
| 18 | Sat 19 Nov 2016 | 50-2 v Boreham WoodBoreham Wood 2-0 Southport | National League |
| 19 | Tue 22 Nov 2016 | 52-2 v ChesterChester 2-2 Southport | National League |
| 20 | Sat 26 Nov 2016 | 54-5 v Braintree TownSouthport 4-5 Braintree Town | National League |
| 21 | Tue 29 Nov 2016 | 50-0 v Solihull MoorsSouthport 0-0 Solihull Moors | National League |
| 22 | Sat 17 Dec 2016 | 54-3 v EastleighSouthport 4-3 Eastleigh | National League |
| 23 | Mon 26 Dec 2016 | 50-1 v WrexhamWrexham 1-0 Southport | National League |
| 24 | Sun 1 Jan 2017 | 53-2 v WrexhamSouthport 3-2 Wrexham | National League |
| 25 | Sat 7 Jan 2017 | 51-2 v Aldershot TownAldershot Town 2-1 Southport | National League |
| 26 | Tue 10 Jan 2017 | 51-0 v BarrowBarrow 0-1 Southport | National League |
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