| Trans Num | Date | Details |
| 2001.4 | 2017-01-22 | Due to a managerial error, San Francisco sends Jim Thome to Ellwood City. |
| 2003.3 | 2020-01-06 | Omaha sends Jamie Moyer and Paul LoDuca to San Francisco for Jim Thome. |
| 2004.4 | 2020-07-13 | Washington Bombers trade Jeff Bagwell, Shannon Stewart, and WAS 2004 #2 to the Omaha Knights for Richard Hidalgo and Jim Thome. |