| 05 Nov 12 | S. Mildenhall Steve Mildenhall |  MillwallMIL | → |  Scunthorpe UnitedSCU | Loan |
| 02 Nov 12 | T. Mkandawire Tamika Mkandawire | MillwallMIL | → |  Southend UnitedSOUT | Loan |
| 01 Nov 12 | A. Smith Adam Smith |  Tottenham HotspurTOT | → | MillwallMIL | Loan |
| 01 Nov 12 | A. Smith Adam Smith | Tottenham HotspurTOT | → | MillwallMIL | Loan |
| 05 Oct 12 | M. Beevers Mark Beevers |  Sheffield WednesdaySHW | → | MillwallMIL | Loan |
| 17 Sept 12 | C. Wood Chris Wood |  West Bromwich AlbionWBA | → | MillwallMIL | Loan |
| 17 Sept 12 | C. Wood Chris Wood | West Bromwich AlbionWBA | → | MillwallMIL | Loan |
| 30 Aug 12 | D. Ward Darren Ward | MillwallMIL | → |  Swindon TownSWI | Loan |
| 13 Aug 12 | D. Shittu Danny Shittu | XXX | → | MillwallMIL | Free |
| 13 Aug 12 | S. Barron Scott Barron | MillwallMIL | → |  BrentfordBRE | Free |
| 01 Aug 12 | C. Hackett Chris Hackett | MillwallMIL | → |  Northampton TownNHT | Free |
| 18 Jul 12 | R. Allsop Ryan Allsop | MillwallMIL | → |  Leyton OrientLEY | Free |
| 13 Jul 12 | K. Osborne Karleigh Osborne | BrentfordBRE | → | MillwallMIL | Free |
| 13 Jul 12 | T. Craig Tony Craig | MillwallMIL | → | BrentfordBRE | Undisclosed |
| 15 Jun 12 | C. Taylor Chris Taylor |  Oldham AthleticOLD | → | MillwallMIL | Free |
| 19 Mar 12 | D. N'Guessan Dany N'Guessan | MillwallMIL | → |  Charlton AthleticCHA | Loan |
| 12 Mar 12 | M. Taylor Maik Taylor |  Leeds UnitedLEE | → | MillwallMIL | Loan |
| 21 Feb 12 | S. Batt Shaun Batt | MillwallMIL | → |  Crawley TownCRA | Loan |
| 21 Feb 12 | C. Hackett Chris Hackett | MillwallMIL | → |  Wycombe WanderersWYC | Loan |
| 31 Jan 12 | A. Keogh Andy Keogh |  Wolverhampton WanderersWOL | → | MillwallMIL | Undisclosed |
| 31 Jan 12 | A. Keogh Andy Keogh | Wolverhampton WanderersWOL | → | MillwallMIL | Undisclosed |
| 27 Jan 12 | S. Lowry Shane Lowry |  Aston VillaAVL | → | MillwallMIL | Undisclosed |
| 27 Jan 12 | S. Lowry Shane Lowry | Aston VillaAVL | → | MillwallMIL | Undisclosed |
| 20 Jan 12 | J. McQuoid Josh McQuoid | MillwallMIL | → |  BurnleyBUR | Loan |
| 05 Jan 12 | D. Purse Darren Purse | MillwallMIL | → |  Plymouth ArgylePLY | Free |
| 01 Jan 12 | R. Mason Ryan Mason | Tottenham HotspurTOT | → | MillwallMIL | Loan |
| 01 Jan 12 | R. Mason Ryan Mason | Tottenham HotspurTOT | → | MillwallMIL | Loan |
| 01 Jan 12 | H. Kane Harry Kane | Tottenham HotspurTOT | → | MillwallMIL | Loan |
| 01 Jan 12 | H. Kane Harry Kane | Tottenham HotspurTOT | → | MillwallMIL | Loan |