| 01 Sept 25 | V. Boniface Victor Boniface |  Bayer LeverkusenB04 | → |  VfL WolfsburgWOB | Loan |
| 01 Sept 25 | P. Hincapié Piero Hincapié | Bayer LeverkusenB04 | → |  ArsenalARS | Loan |
| 01 Sept 25 | E. Fernández Ezequiel Fernández |  Al QadsiahQAD | → | Bayer LeverkusenB04 | Undisclosed |
| 01 Sept 25 | G. Puerta Gustavo Puerta | Bayer LeverkusenB04 | → |  Racing SantanderRAC | Undisclosed |
| 31 Aug 25 | E. Ben Seghir Eliesse Ben Seghir |  AS MonacoMON | → | Bayer LeverkusenB04 | Undisclosed |
| 26 Aug 25 | L. Vázquez Lucas Vázquez |  Real MadridRMA | → | Bayer LeverkusenB04 | Free |
| 21 Aug 25 | A. Adli Amine Adli | Bayer LeverkusenB04 | → |  AFC BournemouthBOU | Undisclosed |
| 21 Aug 25 | C. Echeverri Claudio Echeverri |  Manchester CityMNC | → | Bayer LeverkusenB04 | Loan |
| 21 Aug 25 | L. Badé Loïc Badé |  SevillaSEV | → | Bayer LeverkusenB04 | Undisclosed |
| 12 Aug 25 | E. Poku Ernest Poku |  AZ AlkmaarAZ | → | Bayer LeverkusenB04 | Undisclosed |
| 11 Aug 25 | J. Blaswich Janis Blaswich |  RB LeipzigRBL | → | Bayer LeverkusenB04 | Undisclosed |
| 08 Aug 25 | L. Hradecky Lukas Hradecky | Bayer LeverkusenB04 | → | AS MonacoMON | Undisclosed |
| 30 Jul 25 | G. Xhaka Granit Xhaka | Bayer LeverkusenB04 | → |  SunderlandSUN | Undisclosed |
| 29 Jul 25 | A. Faye Abdoulaye Faye | Bayer LeverkusenB04 | → |  LorientLOR | Loan |
| 15 Jul 25 | M. Kovar Matej Kovar | Bayer LeverkusenB04 | → |  PSV EindhovenPSV | Loan |
| 12 Jul 25 | M. Tillman Malik Tillman | PSV EindhovenPSV | → | Bayer LeverkusenB04 | Undisclosed |
| 11 Jul 25 | C. Kofane Christian Kofane |  AlbaceteALB | → | Bayer LeverkusenB04 | Undisclosed |
| 02 Jul 25 | J. Quansah Jarell Quansah |  LiverpoolLIV | → | Bayer LeverkusenB04 | Undisclosed |
| 01 Jul 25 | A. Tape Axel Tape |  Paris Saint-GermainPSG | → | Bayer LeverkusenB04 | Free |
| 01 Jul 25 | F. Wirtz Florian Wirtz | Bayer LeverkusenB04 | → | LiverpoolLIV | Undisclosed |
| 01 Jul 25 | O. Kossounou Odilon Kossounou | Bayer LeverkusenB04 | → |  AtalantaATA | Undisclosed |
| 01 Jul 25 | G. Puerta Gustavo Puerta | Bayer LeverkusenB04 | → |  Hull CityHUL | Undisclosed |
| 01 Jul 25 | A. Faye Abdoulaye Faye |  BK HäckenBKH | → | Bayer LeverkusenB04 | Undisclosed |
| 01 Jul 25 | I. Maza Ibrahim Maza |  Hertha BerlinBSC | → | Bayer LeverkusenB04 | Undisclosed |
| 01 Jul 25 | T. Oermann Tim Oermann | Bayer LeverkusenB04 | → |  SK Sturm GrazSTG | Loan |
| 01 Jul 25 | F. Onyeka Francis-Ikechukwu Onyeka | Bayer LeverkusenB04 | → |  VfL BochumBOC | Loan |
| 01 Jul 25 | A. Stepanov Artem Stepanov | Bayer LeverkusenB04 | → |  1. FC NürnbergFCN | Loan |
| 09 Jun 25 | J. Tah Jonathan Tah | Bayer LeverkusenB04 | → |  Bayern MunichMUN | Undisclosed |
| 03 Jun 25 | M. Flekken Mark Flekken |  BrentfordBRE | → | Bayer LeverkusenB04 | Undisclosed |
| 01 Jun 25 | T. Oermann Tim Oermann | VfL BochumBOC | → | Bayer LeverkusenB04 | Undisclosed |
| 01 Jun 25 | J. Frimpong Jeremie Frimpong | Bayer LeverkusenB04 | → | LiverpoolLIV | Undisclosed |
| 03 Feb 25 | N. Mbamba Noah Mbamba | Bayer LeverkusenB04 | → | DXXDenderDEN | Loan |
| 31 Jan 25 | M. Hermoso Mario Hermoso |  AS RomaROMA | → | Bayer LeverkusenB04 | Loan |
| 29 Jan 25 | E. Buendía Emiliano Buendía |  Aston VillaAVL | → | Bayer LeverkusenB04 | Loan |
| 11 Jan 25 | S. Fofana Sadik Fofana | Bayer LeverkusenB04 | → | SK Sturm GrazSTG | Undisclosed |
| 02 Jan 25 | A. Sarco Alejo Sarco |  Vélez SarsfieldVEL | → | Bayer LeverkusenB04 | Free |