| 17 Oct 12 | S. McManus Stephen McManus |  MiddlesbroughMID | → |  Bristol CityBRC | Loan |
| 09 Oct 12 | C. Wyke Charlie Wyke | MiddlesbroughMID | → |  Hartlepool UnitedHAR | Loan |
| 11 Sept 12 | A. Bikey André Bikey | XXX | → | MiddlesbroughMID | Free |
| 29 Aug 12 | J. Bennett Joe Bennett | MiddlesbroughMID | → |  Aston VillaAVL | Undisclosed |
| 29 Aug 12 | J. Bennett Joe Bennett | MiddlesbroughMID | → | Aston VillaAVL | Undisclosed |
| 24 Aug 12 | I. Miller Ishmael Miller |  Nottingham ForestFOR | → | MiddlesbroughMID | Loan |
| 20 Aug 12 | J. McEachran Josh McEachran |  ChelseaCHE | → | MiddlesbroughMID | Loan |
| 20 Aug 12 | J. McEachran Josh McEachran | ChelseaCHE | → | MiddlesbroughMID | Loan |
| 14 Aug 12 | B. Gibson Ben Gibson | MiddlesbroughMID | → |  Tranmere RoversTRN | Loan |
| 13 Aug 12 | J. Leutwiler Jayson Leutwiler |  FC BaselBAS | → | MiddlesbroughMID | Loan |
| 01 Aug 12 | M. Carayol Mustapha Carayol |  Bristol RoversBRI | → | MiddlesbroughMID | Undisclosed |
| 30 Jul 12 | G. Friend George Friend |  Doncaster RoversDON | → | MiddlesbroughMID | Undisclosed |
| 30 Jul 12 | T. McMahon Tony McMahon | MiddlesbroughMID | → |  Sheffield UnitedSHU | Free |
| 10 Jul 12 | E. Ledesma Emmanuel Ledesma |  WalsallWAL | → | MiddlesbroughMID | Free |
| 06 Jul 12 | J. Woodgate Jonathan Woodgate |  Stoke CitySTK | → | MiddlesbroughMID | Free |
| 06 Jul 12 | J. Woodgate Jonathan Woodgate | Stoke CitySTK | → | MiddlesbroughMID | Free |
| 04 Jul 12 | Christian Burgess | XXX | → | MiddlesbroughMID | Free |
| 02 Jul 12 | S. Parnaby Stuart Parnaby | XXX | → | MiddlesbroughMID | Free |
| 02 Jul 12 | J. Grounds Jonathan Grounds | MiddlesbroughMID | → |  Oldham AthleticOLD | Free |
| 01 Jul 12 | G. Leadbitter Grant Leadbitter |  Ipswich TownIPS | → | MiddlesbroughMID | Free |
| 17 May 12 | J. Franks Jonathan Franks | MiddlesbroughMID | → | Hartlepool UnitedHAR | Free |
| 27 Apr 12 | C. Ripley Connor Ripley | MiddlesbroughMID | → |  Oxford UnitedOXF | Loan |
| 01 Mar 12 | A. Hammill Adam Hammill |  Wolverhampton WanderersWOL | → | MiddlesbroughMID | Loan |
| 01 Mar 12 | A. Hammill Adam Hammill | Wolverhampton WanderersWOL | → | MiddlesbroughMID | Loan |
| 22 Feb 12 | J. Grounds Jonathan Grounds | MiddlesbroughMID | → |  Yeovil TownYEO | Loan |
| 22 Feb 12 | J. Franks Jonathan Franks | MiddlesbroughMID | → | Yeovil TownYEO | Loan |
| 14 Feb 12 | S. McManus Stephen McManus | MiddlesbroughMID | → | Bristol CityBRC | Loan |
| 17 Jan 12 | L. Jutkiewicz Lukas Jutkiewicz |  Coventry CityCOV | → | MiddlesbroughMID | Undisclosed |
| 14 Jan 12 | L. Jutkiewicz Lukas Jutkiewicz | Coventry CityCOV | → | MiddlesbroughMID | Loan |