| 1 | Mon 5 Sep 2016 | 1-2 v Chelmsford CityChelmsford City 2-1 Ebbsfleet United | National League South |
| 2 | Sat 22 Oct 2016 | 1-1 v East Thurrock UnitedEast Thurrock United 1-1 Ebbsfleet United | National League South |
| 3 | Sat 19 Nov 2016 | 2-3 v Maidenhead UnitedEbbsfleet United 2-3 Maidenhead United | National League South |
| 4 | Tue 22 Nov 2016 | 1-1 v Hampton & Richmond BoroughEbbsfleet United 1-1 Hampton & Richmond Borough | National League South |
| 5 | Sat 25 Feb 2017 | 1-0 v Bath CityBath City 0-1 Ebbsfleet United | National League South |
| 6 | Sat 4 Mar 2017 | 6-1 v East Thurrock UnitedEbbsfleet United 6-1 East Thurrock United | National League South |
| 7 | Sat 11 Mar 2017 | 3-0 v St Albans CitySt Albans City 0-3 Ebbsfleet United | National League South |
| 8 | Sat 18 Mar 2017 | 2-1 v Weston-super-MareEbbsfleet United 2-1 Weston-super-Mare | National League South |
| 9 | Sat 1 Apr 2017 | 5-1 v Welling UnitedEbbsfleet United 5-1 Welling United | National League South |
| 10 | Sat 8 Apr 2017 | 1-1 v Truro CityTruro City 1-1 Ebbsfleet United | National League South |
| 11 | Sat 29 Apr 2017 | 1-0 v Oxford CityEbbsfleet United 1-0 Oxford City | National League South |
| 12 | Wed 3 May 2017 | 2-1 v Hampton & Richmond BoroughHampton & Richmond Borough 1-2 Ebbsfleet United | National League South Play-off |
| 13 | Sat 13 May 2017 | 2-1 v Chelmsford CityEbbsfleet United 2-1 Chelmsford City | National League South Play-off |
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