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| 2006-05-04 16:40:00 | New York Warriors | Barrett Lee | Acquired via waivers | | Waiver |
| 2006-05-04 16:40:00 | Charlotte Rangers | Milo Downes | Acquired via waivers | | Waiver |
| 2006-05-04 14:00:00 | St. Louis 5th Alarm | Isaiah Perdue | Acquired via trade | 1st round pick in season 14 | San Francisco Golden Gators |
| 2006-05-04 14:00:00 | St. Louis 5th Alarm | Perry Moser | Acquired via trade | 3rd round pick in season 14 | San Francisco Golden Gators |
| 2006-05-04 14:00:00 | St. Louis 5th Alarm | James Trice | Acquired via trade | 3rd round pick in season 14 | San Francisco Golden Gators |
| 2006-05-04 14:00:00 | St. Louis 5th Alarm | Deon Cornett | Acquired via trade | 3rd round pick in season 15 | San Francisco Golden Gators |
| 2006-05-04 14:00:00 | St. Louis 5th Alarm | Dalton Tomes | Acquired via trade | | San Francisco Golden Gators |
| 2006-05-04 12:41:04 | New Orleans Hurricanes | | Drop | Linus Ingle | |
| 2006-05-04 12:36:24 | New Orleans Hurricanes | | Drop | Tyron Penick | |
| 2006-05-04 11:12:16 | San Francisco Golden Gators | | Drop | Trent Maher | |
| 2006-05-04 10:59:38 | New Orleans Hurricanes | | Drop | Neil Eagle | |
| 2006-05-04 10:58:12 | San Francisco Golden Gators | | Drop | Woodrow Priest | |
| 2006-05-04 10:56:02 | New Orleans Hurricanes | | Drop | Solomon Garvey | |
| 2006-05-04 10:21:32 | New Orleans Hurricanes | | Drop | Sven Bird | |
| 2006-05-04 09:56:14 | San Francisco Golden Gators | | Drop | Terrell Lyle | |
| 2006-05-04 09:48:00 | Cincinnati Skyliners | | Drop | Quin Cundiff | |
| 2006-05-04 09:45:04 | San Francisco Golden Gators | | Drop | Owen Dahlem | |
| 2006-05-04 09:30:44 | Cincinnati Skyliners | | Drop | Clem Proffitt | |
| 2006-05-04 06:09:38 | Salt Lake City Night Hawks | Eric Lyvers | Add/Drop | Leslie Schall | |
| 2006-05-04 06:05:46 | Salt Lake City Night Hawks | | Drop | Tyler Byrne | |
| 2006-05-04 01:56:06 | Houston Octopods | | Drop | Alexander Dutton | |
| 2006-05-04 00:16:42 | Atlanta Eels | | Drop | Dustin Rizo | |
| 2006-05-04 00:15:18 | Atlanta Eels | | Drop | Shaun West | |
| 2006-05-03 19:21:36 | Indianapolis Tornadoes | | Drop | Shane Moss | |
| 2006-05-03 19:21:06 | Indianapolis Tornadoes | | Drop | Tandre Canter | |