| 19 Sept 16 | N. Colazo Nicolás Colazo |  Boca JuniorsCABJ | → |  Melbourne City FCMCY | Loan |
| 19 Sept 16 | N. Colazo Nicolás Colazo | Boca JuniorsCABJ | → | Melbourne City FCMCY | Loan |
| 01 Sept 16 | M. Jakobsen Michael Jakobsen |  Esbjerg FBESBJ | → | Melbourne City FCMCY | Undisclosed |
| 10 Aug 16 | T. Cahill Tim Cahill |  Zhejiang Professional FCZHE | → | Melbourne City FCMCY | Free |
| 18 Jul 16 | N. Kilkenny Neil Kilkenny |  Preston North EndPNE | → | Melbourne City FCMCY | Free |
| 18 Jul 16 | N. Kilkenny Neil Kilkenny | Preston North EndPNE | → | Melbourne City FCMCY | Free |
| 01 Jul 16 | H. Novillo Harry Novillo | Melbourne City FCMCY | → | MXXManisasporManisaspor | 500000 |
| 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 | A. Mooy Aaron Mooy | Melbourne City FCMCY | → | Manchester CityMNC | Undisclosed |
| 01 Jul 16 | L. Brattan Luke Brattan | Manchester CityMNC | → | Melbourne City FCMCY | Loan |
| 06 May 16 | B. Kamau Bruce Kamau |  Adelaide UnitedADE | → | Melbourne City FCMCY | Free |
| 05 Feb 16 | A. Wilkinson Alex Wilkinson | JMXJeonbuk MotorsJeonbuk Motors | → | Melbourne City FCMCY | Free |
| 19 Jan 16 | A. Cáceres Anthony Cáceres | Manchester CityMNC | → | Melbourne City FCMCY | Loan |
| 19 Jan 16 | A. Cáceres Anthony Cáceres | Manchester CityMNC | → | Melbourne City FCMCY | Loan |