| Season: | 1998–99 |
| Competition: | A Lyga |
| Winners: | FK Zalgiris |
| Relegated: | Zalgiris-2 Vilnius Kauno Jegarai FK Lokomotyvas Mastis Telsiai |
| Continentalcup1: | UEFA Champions League |
| Continentalcup1 Qualifiers: | FK Zalgiris |
| Continentalcup2: | UEFA Cup |
| Continentalcup2 Qualifiers: | Kareda Siauliai FBK Kaunas |
| Continentalcup3: | UEFA Intertoto Cup |
| Continentalcup3 Qualifiers: | FK Ekranas |
| Prevseason: | 1997–98 |
| Nextseason: | 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.[1] 13 teams participated and FK Žalgiris Vilnius won the championship.
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