| 21 Nov 13 | M. Friedrich Manuel Friedrich | XXX | → |  Borussia DortmundDOR | Free |
| 22 Jul 13 | M. Bakalorz Marvin Bakalorz | Borussia DortmundDOR | → |  Eintracht FrankfurtSGE | Undisclosed |
| 09 Jul 13 | H. Mkhitaryan Henrikh Mkhitaryan | SDXShakhtar DonetskShakhtar Donetsk | → | Borussia DortmundDOR | 23675000 |
| 04 Jul 13 | P. Aubameyang Pierre-Emerick Aubameyang |  Saint-EtienneASSE | → | Borussia DortmundDOR | Undisclosed |
| 04 Jul 13 | P. Aubameyang Pierre-Emerick Aubameyang | Saint-EtienneASSE | → | Borussia DortmundDOR | Undisclosed |
| 01 Jul 13 | M. Götze Mario Götze | Borussia DortmundDOR | → |  Bayern MunichMUN | 31500000 |
| 01 Jul 13 | Hendrik Bonmann | REXRot-Weiss EssenRot-Weiss Essen | → | Borussia DortmundDOR | Free |
| 01 Jul 13 | Kerem Demirbay | Borussia DortmundDOR | → |  Hamburg SVHSV | Free |
| 01 Jul 13 | Nick Weber | Borussia DortmundDOR | → |  NurnbergNUR | Free |
| 01 Jul 13 | M. Leitner Moritz Leitner | Borussia DortmundDOR | → |  VfB StuttgartVFB | Loan |
| 17 Jun 13 | L. Bittencourt Leonardo Bittencourt | Borussia DortmundDOR | → |  Hannover 96HAN | Undisclosed |
| 10 Jun 13 | J. Koch Julian Koch | Borussia DortmundDOR | → |  MainzMAIN | Undisclosed |
| 06 Jun 13 | D. Ginczek Daniel Ginczek | Borussia DortmundDOR | → | NurnbergNUR | Undisclosed |
| 28 May 13 | S. Papastathopoulos Sokratis Papastathopoulos |  Werder BremenWER | → | Borussia DortmundDOR | Undisclosed |
| 28 May 13 | F. Santana Felipe Santana | Borussia DortmundDOR | → |  Schalke 04SCHA | Undisclosed |
| 12 Jan 13 | C. Löwe Chris Löwe | Borussia DortmundDOR | → |  KaiserslauternFCK | Undisclosed |
| 11 Jan 13 | N. Sahin Nuri Sahin |  Real MadridMAD | → | Borussia DortmundDOR | Loan |
| 11 Jan 13 | N. Sahin Nuri Sahin | Real MadridMAD | → | Borussia DortmundDOR | Loan |
| 06 Jan 13 | I. Perisic Ivan Perisic | Borussia DortmundDOR | → |  VfL WolfsburgWOB | Undisclosed |
| 01 Jan 13 | Marian Sarr |  Bayer LeverkusenLEV | → | Borussia DortmundDOR | Undisclosed |