| Season: | 2006 |
| Dates: | 15 April-12 November |
| Competition: | A Lyga |
| Winners: | FBK Kaunas |
| Relegated: | FK Silute FK Nevezis |
| Continentalcup1: | UEFA Champions League |
| Continentalcup1 Qualifiers: | FBK Kaunas |
| Continentalcup2: | UEFA Cup |
| Continentalcup2 Qualifiers: | FK Ekranas FK Suduva |
| Continentalcup3: | UEFA Intertoto Cup |
| Continentalcup3 Qualifiers: | FK Vetra |
| League Topscorer: |  Serhiy Kuznetsov (18 goals) |
| Prevseason: | 2005 |
| Nextseason: | 2007 |
The Lithuanian A Lyga 2006 was the 17th season of top-tier football in Lithuania. The season started on 15 April 2006 and ended on 12 November 2006.[1] 10 teams participated with FBK Kaunas winning the championship.
|}
| Pos. | Player | Club | Goals | |
|---|---|---|---|---|
| 1 | Serhiy Kuznetsov | Vėtra | 18 | |
| 2 |  Mantas Savėnas | Ekranas | 16 | |
| Ilya Halyuza | Šiauliai | |||
| 4 | Andrius Velička | FBK Kaunas | 14 | |
| Ričardas Beniušis | FBK Kaunas | |||
| 6 | Povilas Lukšys | Ekranas | 13 | |
| Maksim Morozov | Atlantas | |||
| Vitalis Stankevičius | Nevėžis | |||
 Edin Pehlić | FBK Kaunas | |||
| 10 | Ekranas | 12 |