| Transactions |
| Date | Team | Player | Type | OthTm | EffDate | When |
| 3/27/2012 | SD | Gardner | Acquired via trade | Tex | | After |
| 4/9/2012 | LAN | Kotsay | Demoted to reserve roster | | | Before |
| 4/9/2012 | LAN | Sutton | Promoted to active roster | | | Before |
| 4/9/2012 | Phi | Aubrey | Demoted to reserve roster | | | Before |
| 4/9/2012 | Phi | Ledezma | Promoted to active roster | | | Before |
| 4/15/2012 | Phi | Hamels | Traded away | Tor | | After |
| 4/15/2012 | Phi | Infante | Traded away | Tor | | After |
| 4/15/2012 | Phi | Melancon | Acquired via trade | Tor | | After |
| 4/15/2012 | Phi | Soria | Traded away | Tor | | After |
| 4/15/2012 | Phi | Vizcaino | Acquired via trade | Tor | | After |
| 4/15/2012 | Phi | Weeks | Acquired via trade | Tor | | After |
| 4/15/2012 | Phi | Werth | Traded away | Tor | | After |
| 4/16/2012 | Phi | Aubrey | Demoted to reserve roster | | | Before |
| 4/16/2012 | Phi | Aubrey | Promoted to active roster | | | Before |
| 4/16/2012 | Phi | Aubrey | Promoted to active roster | | | Before |
| 4/16/2012 | Phi | Leroux | Promoted to active roster | | | Before |
| 4/16/2012 | Phi | Rhymes | Demoted to reserve roster | | | Before |
| 4/16/2012 | Phi | Rhymes | Promoted to active roster | | | Before |
| 4/16/2012 | Phi | Vizcaino | Demoted to reserve roster | | | Before |
| 4/16/2012 | Pit | Sweeney | Promoted to active roster | | | Before |
| 4/16/2012 | Pit | Valencia | Demoted to reserve roster | | | Before |
| 4/16/2012 | Pit | Westbrook | Signed | | | Before |
| 4/16/2012 | Pit | Westbrook | Demoted to reserve roster | | | Before |
| 4/22/2012 | Col | Cortes | Traded away | LAA | | After |
| 4/22/2012 | Col | Sonnanstine | Traded away | ChA | | After |
| 4/22/2012 | Col | Veal | Traded away | StL | | After |
| 4/22/2012 | Phi | Dempster | Traded away | KC | | After |
| 4/22/2012 | Phi | Soriano | Acquired via trade | KC | | After |
| 4/22/2012 | StL | Veal | Acquired via trade | Col | | After |
| 4/23/2012 | Cin | Buchholz | Placed on disabled list | | 4/21/2012 | Before |
| 4/23/2012 | Cin | Moseley | Promoted to active roster | | | Before |
| 4/23/2012 | Col | Clement | Placed on disabled list | | 4/19/2012 | Before |
| 4/23/2012 | Col | Flowers | Promoted to active roster | | | Before |
| 4/23/2012 | SF | Bogusevic | Promoted to active roster | | | Before |
| 4/23/2012 | SF | Lewis | Placed on disabled list | | 4/19/2012 | Before |
| 4/29/2012 | StL | Cordero | Acquired via trade | KC | | After |
| 4/29/2012 | StL | Jenks | Acquired via trade | KC | | After |
| 4/29/2012 | StL | Korecky | Traded away | KC | | After |
| 4/29/2012 | StL | Morrison | Traded away | KC | | After |
| 4/29/2012 | StL | Reyes | Traded away | KC | | After |
| 4/29/2012 | StL | Takahashi | Acquired via trade | KC | | After |
| 4/30/2012 | Phi | Aubrey | Demoted to reserve roster | | | Before |
| 4/30/2012 | Phi | Daley | Signed | | | Before |
| 4/30/2012 | SF | Castillo | Signed | | | Before |
| 4/30/2012 | StL | Corpas | Demoted to reserve roster | | | Before |
| 4/30/2012 | StL | Williams | Demoted to reserve roster | | | Before |
| 5/6/2012 | Cin | Nathan | Acquired via trade | Bal | | After |
| 5/6/2012 | Hou | Kennedy | Acquired via trade | Bal | | After |
| 5/6/2012 | Hou | Norris | Traded away | Bal | | After |
| 5/6/2012 | Hou | Pomeranz | Traded away | Bal | | After |
| 5/6/2012 | Hou | Valverde | Acquired via trade | Bal | | After |
| 5/7/2012 | Atl | Huffman | Promoted to active roster | | | Before |
| 5/7/2012 | Atl | Pagan | Placed on disabled list | | 5/6/2012 | Before |
| 5/7/2012 | Cin | Freeman | Demoted to reserve roster | | | Before |
| 5/7/2012 | Hou | Leake | Demoted to reserve roster | | | Before |
| 5/7/2012 | SF | Bogusevic | Demoted to reserve roster | | | Before |
| 5/7/2012 | StL | Badenhop | Placed on disabled list | | 5/2/2012 | Before |
| 5/7/2012 | StL | Corpas | Promoted to active roster | | | Before |
| 5/7/2012 | Was | Beato | Demoted to reserve roster | | | Before |
| 5/7/2012 | Was | Blum | Signed | | | Before |
| 5/13/2012 | ChN | Manship | Traded away | KC | | After |
| 5/13/2012 | Pit | Bailey | Acquired via trade | Tor | | After |
| 5/13/2012 | Pit | Crisp | Acquired via trade | Was | | After |
| 5/13/2012 | Pit | Shields | Traded away | Tor | | After |
| 5/13/2012 | Pit | Torres | Traded away | Was | | After |
| 5/13/2012 | StL | Atchison | Acquired via trade | Tam | | After |
| 5/13/2012 | StL | Chen | Traded away | Tam | | After |
| 5/13/2012 | StL | Gonzalez | Acquired via trade | LAA | | After |
| 5/13/2012 | Was | Crisp | Traded away | Pit | | After |
| 5/13/2012 | Was | Hart | Acquired via trade | LAA | | After |
| 5/13/2012 | Was | McDonald | Traded away | Bal | | After |
| 5/13/2012 | Was | Torres | Acquired via trade | Pit | | After |
| 5/14/2012 | Ari | Owings | Promoted to active roster | | | Before |
| 5/14/2012 | Ari | Pestano | Placed on disabled list | | 5/14/2012 | Before |
| 5/14/2012 | Cin | Buchholz | Activated from disabled list | | | Before |
| 5/14/2012 | Cin | Freeman | Promoted to active roster | | | Before |
| 5/14/2012 | Cin | Grilli | Demoted to reserve roster | | | Before |
| 5/14/2012 | Cin | Moseley | Demoted to reserve roster | | | Before |
| 5/14/2012 | Hou | Cantu | Demoted to reserve roster | | | Before |
| 5/14/2012 | Hou | Jaso | Promoted to active roster | | | Before |
| 5/14/2012 | Hou | Leake | Promoted to active roster | | | Before |
| 5/14/2012 | Hou | Teheran | Placed on disabled list | | 5/9/2012 | Before |
| 5/14/2012 | StL | Takahashi | Demoted to reserve roster | | | Before |
| 5/14/2012 | Was | Beato | Promoted to active roster | | | Before |
| 5/14/2012 | Was | Blum | Demoted to reserve roster | | | Before |