| 31 Aug 16 | J. Bandowski Jannik Bandowski |  Borussia DortmundDOR | → |  VfL BochumBOC | Undisclosed |
| 12 Aug 16 | M. Leitner Moritz Leitner | Borussia DortmundDOR | → |  LazioLAZ | Undisclosed |
| 12 Aug 16 | M. Leitner Moritz Leitner | Borussia DortmundDOR | → | LazioLAZ | Undisclosed |
| 01 Aug 16 | J. Blaszczykowski Jakub Blaszczykowski | Borussia DortmundDOR | → |  VfL WolfsburgWOB | Undisclosed |
| 22 Jul 16 | A. Schürrle André Schürrle | VfL WolfsburgWOB | → | Borussia DortmundDOR | Undisclosed |
| 21 Jul 16 | M. Götze Mario Götze |  Bayern MunichMUN | → | Borussia DortmundDOR | Undisclosed |
| 08 Jul 16 | J. Stankovic Jon Gorenc Stankovic | Borussia DortmundDOR | → |  Huddersfield TownHUD | Undisclosed |
| 08 Jul 16 | J. Stankovic Jon Gorenc Stankovic | Borussia DortmundDOR | → | Huddersfield TownHUD | Undisclosed |
| 06 Jul 16 | H. Mkhitaryan Henrikh Mkhitaryan | Borussia DortmundDOR | → |  Manchester UnitedMAN | Undisclosed |
| 06 Jul 16 | H. Mkhitaryan Henrikh Mkhitaryan | Borussia DortmundDOR | → | Manchester UnitedMAN | Undisclosed |
| 01 Jul 16 | R. Guerreiro Raphaël Guerreiro |  LorientLOR | → | Borussia DortmundDOR | Undisclosed |
| 01 Jul 16 | O. Dembélé Ousmane Dembélé |  Stade RennaisREN | → | Borussia DortmundDOR | Undisclosed |
| 01 Jul 16 | R. Guerreiro Raphaël Guerreiro | LorientLOR | → | Borussia DortmundDOR | Undisclosed |
| 01 Jul 16 | I. Gündogan Ilkay Gündogan | Borussia DortmundDOR | → |  Manchester CityMNC | Undisclosed |
| 01 Jul 16 | E. Mor Emre Mor |  FC NordsjaellandNORD | → | Borussia DortmundDOR | Undisclosed |
| 01 Jul 16 | O. Dembélé Ousmane Dembélé | Stade RennaisREN | → | Borussia DortmundDOR | Undisclosed |
| 01 Jul 16 | I. Gündogan Ilkay Gündogan | Borussia DortmundDOR | → | Manchester CityMNC | Undisclosed |
| 06 Jun 16 | S. Rode Sebastian Rode | Bayern MunichMUN | → | Borussia DortmundDOR | Undisclosed |
| 23 May 16 | M. Hummels Mats Hummels | Borussia DortmundDOR | → | Bayern MunichMUN | Undisclosed |
| 14 Jan 16 | C. Immobile Ciro Immobile | Borussia DortmundDOR | → |  TorinoTOR | Loan |
| 14 Jan 16 | C. Immobile Ciro Immobile | Borussia DortmundDOR | → | TorinoTOR | Loan |
| 02 Jan 16 | J. Hofmann Jonas Hofmann | Borussia DortmundDOR | → |  Borussia MonchengladbachMON | Undisclosed |