1998–99 A Lyga
| Season | 1998–99 |
|---|---|
| Champions | FK Zalgiris |
| Relegated | Zalgiris-2 Vilnius Kauno Jegarai FK Lokomotyvas Mastis Telsiai |
| UEFA Champions League | FK Zalgiris |
| UEFA Cup | Kareda Siauliai FBK Kaunas |
| UEFA Intertoto Cup | FK Ekranas |
← 1997–98 1999 → | |
The Lithuanian A Lyga 1998–99 was the ninth season of top-tier football in Lithuania. The season started on 10 July 1998 and ended on 13 June 1999. 13 teams participated and FK Žalgiris Vilnius won the championship.