Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/1999 |  | Mindaugas Pacevičius | DF |  | Kauno Jegeriai | Kauno Jegeriai |
| 01/1999 | | Darius Regelskis | DF | |||
| 01/1999 |  | Aleksandrs Stradiņš | DF |  | FK Ventspils | FK Ventspils |
| 01/1999 | | Dainius Suliauskas | DF |  | GKS Bełchatów | GKS Bełchatów |
| 01/1999 | | Raimundas Vainoras | DF |  | Sokol Saratov | Sokol Saratov |
| 01/1999 | | Giedrius Žutautas | DF |  | Spartak Nalchik | Nalchik |
| 01/1999 | | Mindaugas Balvočius | MF | |||
| 01/1999 |  | Aleksey Prokhorenkov | FW |  | Dinamo Moskva | Din. Moskva |
| 01/1999 | | Audrius Šlekys | FW |  | Spartak Vladikavkaz | Spartak |
| 09/1998 | | Vadimas Petrenko | MF |  | Inkaras Kaunas | Inkaras Kaunas |
| 07/1998 | | Vytautas Karvelis | FW |  | Lokomotyvas Vilnius | Lokomotyvas Vilnius |
| 07/1998 | | Valdas Trakys | FW |  | KRC Zuid-West-Vlaanderen | KRC ZWV |
| 07/1998 | | Šenderis Giršovicius | MA |  | Kareda Kaunas | Kareda Kaunas |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/1999 | | Modestas Stonys | GK | | Kauno Jegeriai | Kauno Jegeriai |
| 01/1999 | | Darius Gvildys | DF |  | Lok. Nizhni Novgorod | Lok. Nizhni Novgorod |
| 01/1999 | | Arturas Jakeliunas | DF |  | FK Rīga | FK Rīga |
| 07/1998 | | Darius Jakubaitis | DF |  | Utenis Utena | Utenis Utena |
| 07/1998 | | Dainius Kunevičius | DF | | Kauno Jegeriai | Kauno Jegeriai |
| 07/1998 | | Tomas Sendzikas | DF |  | FK Nevėžis | FK Nevėžis |
| 07/1998 | | Robertas Žalys | FW | | FK Nevėžis | FK Nevėžis |