Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 07/2006 |  | Andrius Bartkus | DF |  | FK Atlantas | Atlantas |
| 07/2006 | | Mindaugas Pacevičius | DF |  | FK Liepājas Metalurgs | Liepājas |
| 04/2006 |  | Muharem Bajrami | MF |  | KF Shkupi | KF Shkupi |
| 01/2006 |  | Mihael Hertelendi | GK |  | NK Domžale | NK Domžale |
| 01/2006 | | Mindaugas Malinauskas | GK |  | FK Žalgiris | Žalgiris |
| 01/2006 |  | José Gonçalves | DF |  | FC Thun Berner Oberland | FC Thun |
| 01/2006 | | Nerijus Radžius | DF |  | Volgar Astrakhan | FK Volgar |
| 01/2006 |  | Maksim Berdnik | MF | |||
| 01/2006 | | Ilgiz Fattakhov | MF | |||
| 01/2006 | | Kęstutis Ivaškevičius | MF |  | FK Šilutė | FK Šilutė |
| 01/2006 | | Gvidas Juška | MF | | FK Šilutė | FK Šilutė |
| 01/2006 | | Audrius Kšanavičius | MF | | FK Atlantas | Atlantas |
| 01/2006 | | Linas Pilibaitis | MF | |||
| 01/2006 |  | Petru Stînga | FW |  | Dacia Chişinău | Dacia Chişinău |
| 01/2006 | | Nerijus Valskis | FW | |||
| 01/2006 |  | Eduard Malofeev | MA |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 09/2006 | | Andrius Velička | FW |  | Heart of Midlothian | Hearts FC |
| 09/2006 | | Kęstutis Ivaškevičius | MF | | Heart of Midlothian | Hearts FC |
| 08/2006 | | Marius Žaliūkas | DF | | Heart of Midlothian | Hearts FC |
| 07/2006 | | Irmantas Zelmikas | DF |  | Tavriya Simferopol (1958-2014) | Tavriya |
| 07/2006 | | Petru Stînga | FW |  | FC Iskra-Stal | Iskra-Stal |
| 01/2006 | | José Gonçalves | DF | | Heart of Midlothian | Hearts FC |
| 01/2006 | | Šarūnas Kilijonas | GK | | FK Šilutė | FK Šilutė |
| 01/2006 | | Nerijus Mačiulis | MF | | FK Šilutė | FK Šilutė |
| 01/2006 | | Tadas Papečkys | MF | | FK Šilutė | FK Šilutė |
| 01/2006 | | Vadimas Petrenko | MF | | FK Šilutė | FK Šilutė |
| 01/2006 | | Tomas Tamošauskas | MF | | FK Liepājas Metalurgs | Liepājas |
| 01/2006 | | Eimantas Poderis | FW | | FK Žalgiris | Žalgiris |
| 01/2006 | | Andrius Puotkalis | FW | | FK Žalgiris | Žalgiris |
| 01/2006 | | Artūras Rimkevičius | FW | | FK Šilutė | FK Šilutė |