| Season: | 1999 |
| Competition: | A Lyga |
| Winners: | FBK Kaunas |
| Continentalcup1: | UEFA Champions League |
| Continentalcup1 Qualifiers: | FBK Kaunas |
| Continentalcup2: | UEFA Cup |
| Continentalcup2 Qualifiers: | FK Zalgiris FK Ekranas |
| Continentalcup3: | UEFA Intertoto Cup |
| Continentalcup3 Qualifiers: | FK Atlantas |
| Prevseason: | 1998–99 |
| Nextseason: | 2000 |
The Lithuanian A Lyga 1999 was the tenth season of top-tier football in Lithuania. The season started on 5 July 1999 and ended on 6 November 1999.[1] 10 teams participated, 3 fewer than the previous season, and Žalgiris Kaunas won the championship.
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