[3] In the following season Neptūnas slightly improved, reaching 10 victories and suffering 30 defeats, with the help of a 21-year-old native Eurelijus Žukauskas, who quickly started becoming the star of the team and later was even nicknamed the "Lithuanian king of blocks".

With Svajūnas Airošius, Aloyzas Vasiliūnas, and Artūras Jakubauskas averaging double-digits in points and Eurelijus Žukauskas often adding solid double-doubles, the team qualified into the LKL playoffs for the first time with 17 victories as the 7th seed.

[9] Despite losing the first series game versus BC Šiauliai 80–69, on April 4, 1997, Neptūnas achieved their first-ever victory in the LKL playoffs in a dominating fashion 88–60.

[12] It was the last game for Eurelijus Žukauskas in a Neptūnas jersey, who, after averaging 15.7 points, 9.8 rebounds and 3.1 blocks, joined Žalgiris and soon became a EuroLeague champion and a multiple medalist with the Lithuania men's national basketball team.

[14] The 1998–1999 season was remarkably different as on October 6, 1998, Neptūnas debuted in the FIBA Korać Cup, their first European tournament during a game versus the Espoon Honka, which they lost 93–73.

[15] But afterwards the team, led by Svajūnas Airošius, Arūnas Seferis and Arvydas Macijauskas, finished with a 4–2 record, claimed the second place in the group and advanced into the sixteenth-finals.

[20] During the following 2001–2002 LKL season, Neptūnas triumphed just 10 times per 32 games, but that was enough to qualify for the LKL playoffs as the 8th seed, although they were quickly wiped out 0–2 by an uprising Lithuanian powerhouse Lietuvos rytas Vilnius, led by young and hungry Ramūnas Šiškauskas, Robertas Javtokas, Simas Jasaitis, Rimantas Kaukėnas and a former Neptūnas player Arvydas Macijauskas.

The aspiration for the first-ever LKL medal was crushed by gallingly losing the series 0–3 to BC Šiauliai, with two home games being lost by just three and two points.

Despite the militant efforts and the thirst for a long-awaited revenge, the series was lost 2–3 following another dramatic defeat of 73–80 in Šiauliai, with Valdas Vasylius and Arvydas Eitutavičius scoring more than half of the team's points (45).

[37] Regardless of being smashed 61–96 in Kaunas during the first series encounter, the team, led by a captain Martynas Mažeika, mightily fought in their home arena, this time losing only 82–88.

In the second-tier European league EuroCup Neptūnas won four games out of ten and after taking fifth place of sixth in the group did not qualify into the second stage.

[57] On October 23, 2014, Neptūnas achieved the club's first EuroLeague victory against KK Crvena zvezda with a score of 83–81 after the Valdas Vasylius winning shot 3 seconds away from over-time.

[59] Despite being competitive and cherishing a chance of qualifying for the TOP16 stage, Neptūnas failed to accomplish this in their debut EuroLeague season, winning 4 games of 10 total and taking 5th place in the group.

They shockingly lost to Juventus in the LKL bronze medals series 2–3, including an embarrassing defeat in the decisive game 69–84 in the home arena.

[80] University of Rhode Island graduate Gilvydas Biruta, who represented the Denver Nuggets during the 2015 NBA Summer League, also joined BC Neptūnas.

[81] Three times Polish league champion and experienced EuroLeague player Daniel Ewing became Neptūnas' main point guard on August 15, 2015.

During the last match of the regular season versus the AEK, Neptūnas was even able to guarantee the first place in the group, but after dissipating a 16-point advantage in the third quarter, lost it 75–71 and finished second.

[89][90] The pleasant 72–68 rematch with Aris left the Neptūnas hopes for the playoffs alive, though it vanished after losing to Alba 62–76 in Berlin and finishing with a 2–4 record in the second round.

The team easily overcame BC Šiauliai 96–58 at the quarter-final, but was powerfully stopped at the semi-final by the upcoming champions Lietuvos rytas Vilnius 97–79.

[104][105] During Game 5, Daniel Ewing led Neptūnas to another stunning upset of the Lithuanian powerhouse 73–72, surprisingly won the intense series 3–2, and advanced into the LKL final just for a second time in club history.

During the 2016–17 LKL Playoffs quarter-final Neptūnas eliminated Juventus Utena 3–0, and advanced into the semi-finals where they faced Lithuanian champions Žalgiris Kaunas.

[141] On November 1, 2017, Neptūnas crushed Gaziantep Basketbol during the Champions League away game 114–73 and achieved their highest victory in the history of the tournament.

Neptūnas also picked up home wins over Lietuvos rytas Vilnius 81:76 and Lietkabelis Panevėžys 86:76, and moved up to 2nd place in the LKL standings.

Neptūnas finished 3rd in the regular season in the LKL, and defeated BC Pieno žvaigždės 3:1 in the quarterfinals, including a dominating 101:64 win in the deciding game four in Pasvalys.

Neptūnas won the Vladas Garastas Cup, defeating BC Dnipro 75–63 in the finals, which also served as the club's 55 year anniversary tournament.

Neptūnas struggled in the LKL, and in February, with an 11–9 record and 5th place in the standings, and an early exit in the Champions League also, replaced coach Rinkevičius with assistant Jurica Žuža.

Under coach Tomas Gaidamavičius, the young team with some veteran leadership, led by players like Martynas Mažeika, Žygimantas Janavičius and Matas Jogėla, were in playoff contention all season long.

Neptūnas signed Sterling Gibbs and Ignas Sargiūnas as the new point guards, Tommy Rutherford and Tim Lambrecht, one of the biggest stars of the LKL the previous season with BC Nevėžis, as well as re-signing Girdžiūnas and Gailius.

Needing changes, Neptūnas made the decision to replace Brazys with longtime Panathinaikos Athens assistant and head coach Georgios Vovoras.

Board Representative Sigitas Ambrazevičius Board members Arunas Tuma Alvydas Vaiciunas Edvinas Vaickus Vytautas Lygnugarys Vidmantas Dambrauskas Director of the Club Sigitas Ambrazevičius Neptūnas closely works with Vladas Knašius Basketball School as a ladder for youth to professional basketball.