| 31 Aug 16 | W. Bony Wilfried Bony |  Manchester CityMNC | → |  Stoke CitySTK | Loan |
| 31 Aug 16 | S. Facey Shay Facey | Manchester CityMNC | → |  HeerenveenHEE | Loan |
| 31 Aug 16 | J. Denayer Jason Denayer | Manchester CityMNC | → |  SunderlandSUN | Loan |
| 31 Aug 16 | Kean Bryan | Manchester CityMNC | → |  BuryBURY | Loan |
| 31 Aug 16 | J. Hart Joe Hart | Manchester CityMNC | → |  TorinoTOR | Loan |
| 31 Aug 16 | S. Nasri Samir Nasri | Manchester CityMNC | → |  SevillaSEV | Loan |
| 31 Aug 16 | E. Mangala Eliaquim Mangala | Manchester CityMNC | → |  ValenciaVAL | Loan |
| 31 Aug 16 | S. Facey Shay Facey | Manchester CityMNC | → | HeerenveenHEE | Loan |
| 31 Aug 16 | S. Nasri Samir Nasri | Manchester CityMNC | → | SevillaSEV | Loan |
| 31 Aug 16 | E. Mangala Eliaquim Mangala | Manchester CityMNC | → | ValenciaVAL | Loan |
| 31 Aug 16 | J. Hart Joe Hart | Manchester CityMNC | → | TorinoTOR | Loan |
| 29 Aug 16 | B. Zuculini Bruno Zuculini | Manchester CityMNC | → |  Rayo VallecanoRAY | Loan |
| 26 Aug 16 | O. Zinchenko Oleksandr Zinchenko | Manchester CityMNC | → |  PSV EindhovenPSV | Loan |
| 26 Aug 16 | O. Zinchenko Oleksandr Zinchenko | Manchester CityMNC | → | PSV EindhovenPSV | Loan |
| 25 Aug 16 | C. Bravo Claudio Bravo |  BarcelonaBAR | → | Manchester CityMNC | Undisclosed |
| 25 Aug 16 | C. Bravo Claudio Bravo | BarcelonaBAR | → | Manchester CityMNC | Undisclosed |
| 16 Aug 16 | M. García Manu García | Manchester CityMNC | → |  AlavésALV | Loan |
| 16 Aug 16 | M. García Manu García | Manchester CityMNC | → | AlavésALV | Loan |
| 13 Aug 16 | G. Glendon George Glendon | Manchester CityMNC | → |  Fleetwood TownFLE | Loan |
| 09 Aug 16 | J. Stones John Stones |  EvertonEVE | → | Manchester CityMNC | Undisclosed |
| 09 Aug 16 | G. Rulli Gerónimo Rulli | Manchester CityMNC | → |  Real SociedadRSO | Loan |
| 09 Aug 16 | G. Rulli Gerónimo Rulli |  Deportivo MaldonadoMAL | → | Manchester CityMNC | Undisclosed |
| 09 Aug 16 | G. Rulli Gerónimo Rulli | Manchester CityMNC | → | Real SociedadRSO | Loan |
| 06 Aug 16 | M. Moreno Marlos Moreno | Manchester CityMNC | → |  Deportivo La CoruñaDEP | Loan |
| 06 Aug 16 | M. Moreno Marlos Moreno | Manchester CityMNC | → | Deportivo La CoruñaDEP | Loan |
| 06 Aug 16 | M. Moreno Marlos Moreno |  Atlético NacionalNAL | → | Manchester CityMNC | Undisclosed |
| 03 Aug 16 | G. Jesus Gabriel Jesus |  PalmeirasPAL | → | Manchester CityMNC | Undisclosed |
| 03 Aug 16 | G. Jesus Gabriel Jesus | Manchester CityMNC | → | PalmeirasPAL | Loan |
| 03 Aug 16 | G. Jesus Gabriel Jesus | PalmeirasPAL | → | Manchester CityMNC | Undisclosed |
| 03 Aug 16 | G. Jesus Gabriel Jesus | Manchester CityMNC | → | PalmeirasPAL | Loan |
| 02 Aug 16 | L. Sané Leroy Sané |  Schalke 04SCHA | → | Manchester CityMNC | Undisclosed |
| 02 Aug 16 | L. Sané Leroy Sané | Schalke 04SCHA | → | Manchester CityMNC | Undisclosed |
| 24 Jul 16 | E. Ünal Enes Ünal | Manchester CityMNC | → |  FC TwenteTWE | Loan |
| 24 Jul 16 | E. Ünal Enes Ünal | Manchester CityMNC | → | FC TwenteTWE | Loan |
| 05 Jul 16 | A. Mooy Aaron Mooy | Manchester CityMNC | → |  Huddersfield TownHUD | Loan |
| 05 Jul 16 | A. Mooy Aaron Mooy | Manchester CityMNC | → | Huddersfield TownHUD | Loan |
| 04 Jul 16 | O. Zinchenko Oleksandr Zinchenko |  FC UfaUFA | → | Manchester CityMNC | Undisclosed |
| 01 Jul 16 | J. Byrne Jack Byrne | Manchester CityMNC | → |  Blackburn RoversBLK | Loan |
| 01 Jul 16 | L. Brattan Luke Brattan | Manchester CityMNC | → |  Melbourne City FCMCY | Loan |
| 01 Jul 16 | S. Fofana Seko Fofana | Manchester CityMNC | → |  UdineseUDN | Undisclosed |
| 01 Jul 16 | Nolito |  Celta VigoCEL | → | Manchester CityMNC | Undisclosed |
| 01 Jul 16 | S. Fofana Seko Fofana | Manchester CityMNC | → | UdineseUDN | Undisclosed |
| 01 Jul 16 | I. Gündogan Ilkay Gündogan |  Borussia DortmundDOR | → | Manchester CityMNC | Undisclosed |
| 01 Jul 16 | J. Byrne Jack Byrne | Manchester CityMNC | → | Blackburn RoversBLK | Loan |
| 01 Jul 16 | A. Mooy Aaron Mooy | Melbourne City FCMCY | → | Manchester CityMNC | Undisclosed |
| 01 Jul 16 | A. Mooy Aaron Mooy | Melbourne City FCMCY | → | Manchester CityMNC | Undisclosed |
| 01 Jul 16 | L. Brattan Luke Brattan | Manchester CityMNC | → | Melbourne City FCMCY | Loan |
| 01 Jul 16 | Nolito | Celta VigoCEL | → | Manchester CityMNC | Undisclosed |
| 01 Jul 16 | I. Gündogan Ilkay Gündogan | Borussia DortmundDOR | → | Manchester CityMNC | Undisclosed |
| 01 Feb 16 | P. Roberts Patrick Roberts | Manchester CityMNC | → |  CelticCEL | Loan |
| 01 Feb 16 | P. Roberts Patrick Roberts | Manchester CityMNC | → | CelticCEL | Loan |
| 19 Jan 16 | G. Evans George Evans | Manchester CityMNC | → |  ReadingREA | Undisclosed |
| 19 Jan 16 | A. Cáceres Anthony Cáceres | Manchester CityMNC | → | Melbourne City FCMCY | Loan |
| 19 Jan 16 | G. Evans George Evans | Manchester CityMNC | → | ReadingREA | Undisclosed |
| 19 Jan 16 | A. Cáceres Anthony Cáceres | Manchester CityMNC | → | Melbourne City FCMCY | Loan |
| 15 Jan 16 | A. Cáceres Anthony Cáceres |  Central Coast MarinersCCM | → | Manchester CityMNC | Undisclosed |
| 15 Jan 16 | A. Cáceres Anthony Cáceres | Central Coast MarinersCCM | → | Manchester CityMNC | Undisclosed |
| 07 Jan 16 | I. Lawlor Ian Lawlor | Manchester CityMNC | → | BuryBURY | Loan |