Žalgiris has featured many Lithuanian football legends during its history including Arminas Narbekovas, Valdas Ivanauskas, Edgaras Jankauskas and Deividas Šemberas.

[4] Steponas Petraitis scored the first official goal for the club that day, beating goalkeeper from a penalty spot in 44th minute.

In the following season they finished fifth and again qualified for UEFA Cup where they faced IFK Göteborg in the first round and Red Star Belgrade in the second.

Despite most of the top players including Arminas Narbekovas, Valdas Ivanauskas, Igoris Pankratjevas, Vyacheslav Sukristov and Robertas Fridrikas leaving the club Žalgiris remained favorites to clinch the Lithuanian title and won A Lyga regular season having lost just once in 32 games.

Žalgiris and Inkaras Kaunas finished the league locked on points at the top and extra match on neutral ground was set to be played.

1995–96 season did not bring silverware either: free scoring Žalgiris side racked up 106 goals in just 28 games in the league yet could only take a third place, six points behind champions Inkaras Kaunas.

Things did not go well in the cup as well as Vilnius' side lost to Kareda Šiauliai in the semi-finals and failed to advance to the final for the first time in six years.

Žalgiris reclaimed the cup in 1996–97 season as Donatas Vencevičius' penalty was enough to see off Inkaras in the final but had to settle for second in the league as Kareda coasted to the title with an 8-point margin.

Defense was the key to success as Žalgiris conceded just 8 goals in 23 games and did not lose a single league match that season.

Under the name of Žalgiris Kaunas they won the transitional shortened league season in 1999 and then backed it up by consecutive titles in 2000, 2001, 2002, 2003 and 2004.

Despite a constant presence in European competitions the results there were rarely encouraging with the aggregate defeats like 2–7 to Ruch Chorzow and 0–7 to Maccabi Tel Aviv.

2005 UEFA Intertoto Cup thus stood out as a major success as green and whites went past three teams – Lisburn Distillery, Dinaburg and Egaleo, before being eliminated by CFR Cluj.

The league finish of fifth could have been seen as adequate for the time (20 points gap to fourth-placed Sūduva was harder to take) but as country's economy braced for the inevitable crisis, expenditures were cut and uncertainty rose Žalgiris was dealt a big blow when club owner Vadim Kastujev was arrested in Moscow.

Striped of funds club survived until the end of the season but failed to meet licensing requirements for top flight competition in 2009.

With FBK Kaunas in complete turmoil and Vėtra bankrupt Ekranas for several years became the undisputed superpower of Lithuanian football.

Moreover, in 2012 Vilnius side finally ended their nine-year trophy drought and won Lithuanian Football Cup, beating Ekranas on penalties following a 0–0 draw.

However, in tense atmosphere it was Atlantas who ultimately let it slip as they could only draw the game with Banga Gargždai and Žalgiris celebrated their first title in fourteen years.

The great year was backed up by successful performance in UEFA Europa League where Vilnius' side eliminated St. Patrick's Athletic, Pyunik Yerevan and Lech Poznan before losing out to Red Bull Salzburg.

Žalgiris finished the season 18 points clear of second-placed Kruoja Pakruojis (the largest winning margin in the league since 2006) and also claimed the cup for the third time in the row, beating Banga Gargždai 2–1 in the final.

The club made return to UEFA Champions League after fourteen-year absence yet it did not bring much joy as Dinamo Zagreb beat Žalgiris 4–0 on aggregate in the second qualifying round.

UEFA Champions League campaign was again limited to just two games as Malmo won the return leg in Vilnius 1–0 after goalless first match in Sweden.

Žalgiris finished the season top of the league, ten points clear of second-placed Trakai thus claiming third successive title.

In the 2016 season, Žalgiris continued its dominance in Lithuanian football in 2016 with fourth consecutive league title and, remarkably, two cup wins.

European experience proved to heartbreaking as following a goalless draw in the first leg in Vilnius Žalgiris was a whisker away from eliminating Astana only to concede an injury time goal to lose the game 2–1.

Žalgiris failed to defend the league title, while they were in top position of the standings until October 2017, but a late march by Sūduva saw them winning their first-ever championship.

João Luís Martins, who became available after the dissolution of FC Stumbras, took on the job of head coach on a temporary basis until the end of the season.

In July 2022, after beating Malmö 3–0 on aggregate in the Champions League second qualifying round, Žalgiris made history by guaranteeing themselves group stage football for the season.

Žalgiris finished the 2023 A Lyga season in second place, twelve points behind winning team FK Panevėžys, who won their first-ever league title.

At the end of the season, Saulius Mikoliūnas, who had been with the club since 2016 and has appeared in over 200 games for Žalgiris, retired from professional football.

[15] Lithuanian Championship: Lithuanian Cup: Lithuanian Super Cup: Soviet Championship: Soviet Top League: Soviet First League: Soviet Second League: Chico Science Cup Baltic League: Summer Universiade: Intertoto Cup: Lithuanian Footballer of the Year A Lyga Player of the Year A Lyga Golden Boot UEFA's Golden Player Lists of the winners of Žalgiris Player of the Year Award instituted from 2004 as voted by the official members of Žalgiris supporters club – Pietų IV: FK Žalgiris players who have either appeared for their respective national team at any time or received an individual award while at the club.