| 1 | Aaron DrinanPenalty goals: 2 | Swindon Town | 22 |
| 2 | Jaze KabiaPenalty goals: 2 | Grimsby Town | 18 |
| 3 | Callum PatersonPenalty goals: 2 | MK Dons | 16 |
| 4 | Isaac HutchinsonPenalty goals: 3 | Cheltenham Town | 16 |
| 4 | Kabongo TshimangaPenalty goals: 3 | Barnet | 16 |
| 6 | Michael CheekPenalty goals: 4 | Bromley | 16 |
| 7 | Alassana JattaPenalty goals: 0 | Notts County | 15 |
| 7 | Daniel KanuPenalty goals: 0 | Walsall | 15 |
| 9 | Matthew DennisPenalty goals: 2 | Notts County | 14 |
| 10 | Callum SteadPenalty goals: 0 | Barnet | 13 |
| 10 | Kieran GreenPenalty goals: 0 | Grimsby Town | 13 |
| 10 | Lee BonisPenalty goals: 0 | Chesterfield | 13 |
| 10 | Nicke KabambaPenalty goals: 0 | Bromley | 13 |
| 14 | Jack PaynePenalty goals: 4 | Colchester United | 13 |
| 15 | Alex GilbeyPenalty goals: 0 | MK Dons | 12 |
| 16 | Fabrizio CavegnPenalty goals: 0 | Bristol Rovers | 11 |
| 16 | Harry AndersonPenalty goals: 0 | Colchester United | 11 |
| 16 | Kyreece LisbiePenalty goals: 0 | Colchester United | 11 |
| 16 | Ryan GraydonPenalty goals: 0 | Salford City | 11 |
| 20 | Ellis HarrisonPenalty goals: 1 | Bristol Rovers | 11 |
| 20 | Josh MarchPenalty goals: 1 | Crewe Alexandra | 11 |
| 22 | Ben KnightPenalty goals: 4 | Cambridge United | 11 |
| 23 | Mark HelmPenalty goals: 1 | Fleetwood Town | 10 |
| 24 | Emre TezgelPenalty goals: 2 | Crewe Alexandra | 10 |
| 25 | Charles VernamPenalty goals: 3 | Grimsby Town | 10 |
| 26 | Charlie WhitakerPenalty goals: 0 | Tranmere Rovers | 9 |
| 26 | Sullay KaikaiPenalty goals: 0 | Cambridge United | 9 |
| 28 | Daniel UdohPenalty goals: 1 | Salford City | 9 |
| 28 | Josh GordonPenalty goals: 1 | Barrow | 9 |
| 30 | Nathaniel Méndez-LaingPenalty goals: 4 | MK Dons | 9 |
| 31 | Ben ThompsonPenalty goals: 0 | Bromley | 8 |
| 31 | Dilan MarkandayPenalty goals: 0 | Chesterfield | 8 |
| 31 | Mike Fondop-TalumPenalty goals: 0 | Oldham Athletic | 8 |
| 31 | Tom NaylorPenalty goals: 0 | Chesterfield | 8 |
| 35 | Ollie PalmerPenalty goals: 1 | Swindon Town | 8 |
| 36 | Harry McKirdyPenalty goals: 2 | Crawley Town | 8 |
| 37 | Jodi JonesPenalty goals: 3 | Notts County | 8 |
| 37 | Mark SheltonPenalty goals: 3 | Barnet | 8 |
| 39 | Aaron PressleyPenalty goals: 0 | Walsall | 7 |
| 39 | Adam SeniorPenalty goals: 0 | Barnet | 7 |
| 39 | Andy CookPenalty goals: 0 | Grimsby Town | 7 |
| 39 | George MillerPenalty goals: 0 | Cheltenham Town | 7 |
| 39 | Isaac FletcherPenalty goals: 0 | Barrow | 7 |
| 39 | Kane DrummondPenalty goals: 0 | Oldham Athletic | 7 |
| 39 | Louis AppéréPenalty goals: 0 | Cambridge United | 7 |
| 39 | Micah MbickPenalty goals: 0 | Colchester United | 7 |
| 39 | Omar SowunmiPenalty goals: 0 | Bromley | 7 |
| 39 | Omari PatrickPenalty goals: 0 | Tranmere Rovers | 7 |
| 39 | Rushian Hepburn-MurphyPenalty goals: 0 | MK Dons | 7 |
| 39 | Shayne LaveryPenalty goals: 0 | Cambridge United | 7 |