* Indicates in-season trade
| Trade # | Team | Traded | To | For |
|---|---|---|---|---|
| 616 | Generals | Jason Bartlett | Reptiles | Yan Gomes |
| 615 | Moondogs | Albert Pujols / Jose Iglesias Emmanuel Burriss |
Reptiles | Adam LaRoche / Brandon Crawford 2013 1st RDP |
| 614 | Colonels | Adam Kennedy | Striders | 2013 5th RDP |
| 613 | Colonels | Drew Butera | Padres | Alex Castellanos |
| 612 | Dynamo | Dale Thayer / 2013 2nd RDP | Warriors | Rafael Soriano |
| 611 | Buskers | 2013 3rd RDP | Striders | Everth Cabrera |
| 610 | Buskers | 2013 4th RDP | Barking Seals | John McDonald |
| 609 | Dynamo | Ben Sheets / Manuel Corpas | Reptiles | Brad Lincoln |
| 608 | Wonder Horses | Scott Hairston / Zach Duke | Redhawks | Lucas Duda |
| 607 | Redhawks | Scott Rolen | Dynamo | 2013 5th RDP |
| 606 | Moondogs | Yonder Alonso | Barking Seals | 2013 1st RDP |
| 605 | Frogs | Jayson Nix / Andruw Jones Drew Sutton |
Redhawks | Elliot Johnson / Trayvon Robinson Ted Lilly |
| 604 | Redhawks | Tyler Chatwood / Rhiner Cruz | Striders | David Ross |
| 603 | Redhawks | Mike Zagurski | T-Bones | Kevin Millwood |
| 602 | Rambler | Lou Marson / 2013 7th RDP | Buskers | 2013 2nd RDP |
| 601 | Redhawks | Chris Carter / Enerio Del Rosario 2013 2nd RDP |
Thunder | Alex Rodriguez / Wade LeBlanc |
| 600 | Redhawks | Jaime Garcia / Vance Worley 2013 1st RDP |
Striders | James Shields |
| 599 | Redhawks | 2013 3rd RDP | Rambler | Casper Wells |
| 598 | Redhawks | Brad Boxberger / Tony Sipp | Striders | Fernando Rodney |
| 597 | Redhawks | Chone Figgins | Roadrunners | Anthony Recker |
| 596 | Rambler | Brandon Kintzler | Roadrunners | Brent Morel |
| 595 | Padres | Garrett Jones / 2013 5th RDP | Aesir | Peter Bourjos / Justin Maxwell |
| 594 | Striders | C.C. Sabathia | Reptiles | Trevor Cahill / 2013 2nd RDP |
| 593 | Sandlappers | Miguel Montero / Corey Kluber Ricky Nicasio |
Oil Barons | J.P. Arencibia / A.J. Griffin Drew Smyly |
| 592 | Farmers | Jesus Flores | Barking Seals | Jose Mijares |
| 591 | Redhawks | Steve Clevenger | Thunder | Chone Figgins |
| 590 | Thunder | Adam Dunn | Padres | 2013 1st RDP |
| 589 | Dynamo | Lucas Duda / Tony Sipp Brad Boxberger |
Redhawks | Josh Willingham / Bobby Abreu |
| 588 | Reptiles | Hank Conger | Blue Sox | 2012 5th RDP (#16) |
| 587 | Terriers | Jeremy Affeldt | Redhawks | Travis Buck / Jeff Manship |
| 586 | Terriers | Martin Maldonado | Striders | Lyle McClellan / Zach Stewart |
| 585 | Redhawks | John Jaso | Frogs | Elliot Johnson |
| 584 | Generals | Bruce Chen | Terriers | Bryan LaHair / Daniel Descalso |
| 583 | Rockets | Erik Bedard | Wonder Horses | Mark Kotsay |
| 582 | Redhawks | David Freese | Jukes | James Russell / Casey Coleman Jeff Keppinger / Jason Castro Vance Worley / Jaime Garcia |
| 581 | Farmers | Pedro Alvarez | Sandlappers | Gavin Floyd / Tony Sipp |
| 580 | Redhawks | Clay Rapada / C.J. Carpenter | Blue Sox | Shawn Camp |
| 579 | Moondogs | Barry Zito / Justin Ruggiano | Aesir | Josh Spence / 2012 1st RDP(#21) |
| 578 | Aesir | Tyler Green | Farmers | Brandon Lyon |
| 577 | Blue Sox | Ryan Dempster | Aesir | Ben Revere |
| 576 | Redhawks | Eric Young | Moondogs | Scott Rolen |
| 575 | Rockets | Chris Nelson | Reptiles | Kendrys Morales |
| 574 | Rockets | Alexi Amarista / 2012 3rd RDP(#22) | Wonder Horses | Joe Nathan |
| 573 | Dynamo | Derek Jeter | Roadrunners | Carlos Beltran / 2012 5th RDP(#28) |
| 572 | Oil Barons | Jhonny Peralta | Buskers | 2012 1st RDP(#26) |
| 571 | T-Bones | Mike Aviles | Sandlappers | Mark Ellis |
| 570 | Redhawks | Brandon McCarthy / Josh Harrison | Barking Seals | Travis Wood |
| 569 | Redhawks | 2012 1st RDP(#6) | Oil Barons | Hiroki Kuroda |