| 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 21 Jan 2017 | 2-0 v Chelmsford CityEbbsfleet United 2-0 Chelmsford City | National League South |
| 6 | Sat 4 Feb 2017 | 4-0 v Concord RangersEbbsfleet United 4-0 Concord Rangers | National League South |
| 7 | Sat 11 Feb 2017 | 3-0 v WhitehawkWhitehawk 0-3 Ebbsfleet United | National League South |
| 8 | Sat 18 Feb 2017 | 1-0 v Hungerford TownEbbsfleet United 1-0 Hungerford Town | National League South |
| 9 | Tue 21 Feb 2017 | 1-1 v Hemel Hempstead TownHemel Hempstead Town 1-1 Ebbsfleet United | National League South |
| 10 | Sat 25 Feb 2017 | 1-0 v Bath CityBath City 0-1 Ebbsfleet United | National League South |
| 11 | Wed 3 May 2017 | 2-1 v Hampton & Richmond BoroughHampton & Richmond Borough 1-2 Ebbsfleet United | National League South Play-off |
| 12 | Sat 13 May 2017 | 2-1 v Chelmsford CityEbbsfleet United 2-1 Chelmsford City | National League South Play-off |
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