| 02 Sept 13 | J. Pohjanpalo Joel Pohjanpalo |  Bayer LeverkusenLEV | → | VAXVfR AalenVfR Aalen | Loan |
| 02 Sept 13 | J. Pohjanpalo Joel Pohjanpalo | HHXHJK HelsinkiHJK Helsinki | → | Bayer LeverkusenLEV | Loan |
| 30 Aug 13 | E. Derdiyok Eren Derdiyok |  TSG HoffenheimHOF | → | Bayer LeverkusenLEV | Loan |
| 30 Aug 13 | A. Milik Arkadiusz Milik | Bayer LeverkusenLEV | → |  FC AugsburgAUG | Loan |
| 21 Aug 13 | K. Bellarabi Karim Bellarabi | Bayer LeverkusenLEV | → |  TSV Eintracht BraunschweigEBS | Loan |
| 02 Aug 13 | E. Can Emre Can |  Bayern MunichMUN | → | Bayer LeverkusenLEV | Undisclosed |
| 20 Jul 13 | Levin Oztunali |  Hamburg SVHSV | → | Bayer LeverkusenLEV | Free |
| 12 Jul 13 | R. Hilbert Roberto Hilbert |  BesiktasBES | → | Bayer LeverkusenLEV | Free |
| 01 Jul 13 | A. Schürrle André Schürrle | Bayer LeverkusenLEV | → |  ChelseaCHE | Undisclosed |
| 01 Jul 13 | D. Carvajal Dani Carvajal | Bayer LeverkusenLEV | → |  Real MadridMAD | 6500000 |
| 01 Jul 13 | E. Spahic Emir Spahic |  SevillaSEV | → | Bayer LeverkusenLEV | Undisclosed |
| 01 Jul 13 | A. Palop Andrés Palop | SevillaSEV | → | Bayer LeverkusenLEV | Free |
| 01 Jul 13 | G. Donati Giulio Donati |  InternazionaleINT | → | Bayer LeverkusenLEV | Undisclosed |
| 01 Jul 13 | D. Carvajal Dani Carvajal | Bayer LeverkusenLEV | → | Real MadridMAD | 6500000 |
| 01 Jul 13 | G. Donati Giulio Donati | InternazionaleINT | → | Bayer LeverkusenLEV | Undisclosed |
| 01 Jul 13 | N. Jørgensen Nicolai Jørgensen | Bayer LeverkusenLEV | → |  FC CopenhagenCOP | Undisclosed |
| 01 Jul 13 | M. Kadlec Michal Kadlec | Bayer LeverkusenLEV | → |  FenerbahceFEN | Undisclosed |
| 01 Jul 13 | A. Schürrle André Schürrle | Bayer LeverkusenLEV | → | ChelseaCHE | Undisclosed |
| 01 Jul 13 | E. Spahic Emir Spahic | SevillaSEV | → | Bayer LeverkusenLEV | Undisclosed |
| 01 Jul 13 | K. Stafylidis Konstantinos Stafylidis |  PAOK SalonikaPAOK | → | Bayer LeverkusenLEV | Undisclosed |
| 01 Jul 13 | A. Palop Andrés Palop | SevillaSEV | → | Bayer LeverkusenLEV | Free |
| 01 Jul 13 | M. Rensing Michael Rensing | Bayer LeverkusenLEV | → |  Fortuna DüsseldorfFOR | Free |
| 01 Jul 13 | D. Schwaab Daniel Schwaab | Bayer LeverkusenLEV | → |  VfB StuttgartVFB | Free |
| 01 Jul 13 | J. Fernándes Junior Fernándes | Bayer LeverkusenLEV | → | DZXDinamo ZagrebDinamo Zagreb | Loan |
| 01 Jul 13 | C. Kramer Christoph Kramer | Bayer LeverkusenLEV | → |  Borussia MonchengladbachMON | Loan |
| 22 Jun 13 | Giulio Donati | InternazionaleINT | → | Bayer LeverkusenLEV | Undisclosed |
| 22 Jun 13 | Giulio Donati | InternazionaleINT | → | Bayer LeverkusenLEV | Undisclosed |
| 17 Jun 13 | S. Heung-Min Son Heung-Min | Hamburg SVHSV | → | Bayer LeverkusenLEV | Undisclosed |
| 29 May 13 | Paul Voss | SEXSW EssenSW Essen | → | Bayer LeverkusenLEV | Undisclosed |
| 29 May 13 | R. Kruse Robbie Kruse | Fortuna DüsseldorfFOR | → | Bayer LeverkusenLEV | Undisclosed |
| 21 May 13 | H. Hosogai Hajime Hosogai | Bayer LeverkusenLEV | → |  Hertha BerlinHERT | Undisclosed |
| 15 Jan 13 | Carlinhos | Bayer LeverkusenLEV | → |  SSV Jahn RegensburgJAHN | Loan |
| 01 Jan 13 | A. Milik Arkadiusz Milik | GZXGornik ZabrzeGornik Zabrze | → | Bayer LeverkusenLEV | Undisclosed |
| 01 Jan 13 | R. Augusto Renato Augusto | Bayer LeverkusenLEV | → |  CorinthiansCOR | Undisclosed |
| 01 Jan 13 | Marian Sarr | Bayer LeverkusenLEV | → |  Borussia DortmundDOR | Undisclosed |
| 01 Jan 13 | Z. Pamic Zvonko Pamic | Bayer LeverkusenLEV | → | DZXDinamo ZagrebDinamo Zagreb | Undisclosed |
| 01 Jan 13 | R. Augusto Renato Augusto | Bayer LeverkusenLEV | → | CorinthiansCOR | Undisclosed |