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| 2006-09-03 16:29:46 | Portland Hipsters | | Drop | Lenny Ebel | |
| 2006-09-03 15:19:56 | Indianapolis Tornadoes | | Drop | Elliott Maupin | |
| 2006-09-03 15:19:06 | Indianapolis Tornadoes | | Drop | Harley Hutchinson | |
| 2006-09-03 13:38:28 | Louisville Colonels | | Drop | Lamond Kays | |
| 2006-09-03 13:37:42 | Louisville Colonels | | Drop | Sheldon Parsons | |
| 2006-09-03 13:12:52 | Memphis Express | | Drop | Kareem Wilkinson | |
| 2006-09-03 13:10:36 | Memphis Express | | Drop | Fred Peterson | |
| 2006-09-02 23:03:54 | Louisville Colonels | | Drop | Antonio Klein | |
| 2006-09-02 18:01:50 | Miami Macho Men | Mathew Alaniz | Add/Drop | | |
| 2006-09-02 17:10:00 | Louisville Colonels | Jamarcus Burton | Acquired via trade | Walter Ballard | Memphis Express |
| 2006-09-02 17:08:00 | San Antonio Brothas | Reuben Jewell | Acquired via trade | Peter Cooke | Philadelphia Assassins |
| 2006-09-02 17:06:00 | San Antonio Brothas | Kerry A. Edwards | Acquired via trade | 1st round pick in season 17 | San Francisco Golden Gators |
| 2006-09-02 17:06:00 | San Antonio Brothas | Malcolm Reynolds | Acquired via trade | | San Francisco Golden Gators |
| 2006-09-02 17:06:00 | San Antonio Brothas | David Cunningham | Acquired via trade | | San Francisco Golden Gators |
| 2006-09-02 17:06:00 | San Antonio Brothas | Jose Darby | Acquired via trade | | San Francisco Golden Gators |
| 2006-09-02 17:04:00 | Phoenix Kangaroos | 1st round pick in season 16 | Acquired via trade | Brenden Hoffman | Philadelphia Assassins |
| 2006-09-02 17:04:00 | Phoenix Kangaroos | Brandon Andrews | Acquired via trade | | Philadelphia Assassins |
| 2006-09-02 17:02:00 | Memphis Express | Irvin Underhill | Acquired via trade | Vincent Barber | Los Angeles Cacti |
| 2006-09-02 17:00:00 | St. Louis 5th Alarm | Charles Conway | Acquired via waivers | | Waiver |
| 2006-09-01 17:24:00 | San Francisco Golden Gators | 2nd round pick in season 15 | Acquired via trade | Felix Tyler | Denver Ferris Wheels |
| 2006-09-01 17:22:00 | Las Vegas Dark Knights | Reggie McAllister | Acquired via trade | Jon Funk | Cleveland Weasels |
| 2006-09-01 17:22:00 | Las Vegas Dark Knights | 2nd round pick in season 15 | Acquired via trade | | Cleveland Weasels |
| 2006-09-01 17:20:00 | San Francisco Golden Gators | Bob Manley | Acquired via trade | 1st round pick in season 15 | Cleveland Weasels |
| 2006-09-01 17:20:00 | San Francisco Golden Gators | 2nd round pick in season 16 | Acquired via trade | 1st round pick in season 16 | Cleveland Weasels |
| 2006-09-01 13:24:24 | Philadelphia Assassins | Wally Lacefield | Add/Drop | | |