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The Perlas club was founded in 2003. Over the decade, the team had many variations of its name, but it always had the word "Perlas" (Pearl) in it except during the 2012–2013 season, when it was called "Vilnius-MRU". It developed young prospects and became a springboard to a professional career for former Lietuvos Rytas Vilnius players, guard Dovydas Redikas and BC Žalgiris former player Mindaugas Kuzminskas. Undoubtedly, Perlas’ best-known alumni is Lietuvos Rytas Vilnius, Memphis Grizzlies and Lithuania men's national basketball team center Jonas Valančiūnas.

"Perlas-MRU" qualified for the second-tier Lithuanian basketball league (NKL) playoffs for the first time in the 2006–2007 season. An ambitious and young team, they went on a commercial basis to play in the LKL in 2009. During two seasons in the league, "Perlas-MRU" finished the regular season in 8th and 7th place, respectively. On 14 July 2011, the club merged with NKL champions „Pieno Žvaigždės“, with many players signing with BC Pieno žvaigždės as a result.

In the 2011–2012 season after returning to the NKL, "Perlas-MRU" did not qualify for the playoffs. In the 2012–2013 season, the results for the team were much better. In the regular season, Vilnius team was ranked 12th (14/20), but in the Round of 16 it eliminated fifth-ranked Sūduva-Mantinga (2–1). In the quarterfinals, "Perlas-MRU" met with Jonavos "Triobet" but was eliminated after three intense matches.

In the 2013–2014 season, Perlas once again qualified for the NKL playoffs. In the round of 16, Mindaugas Sakalauskas players crushed Klaipedos Nafta-Universitetas (3–0), but in quarterfinals, they were forced to concede to Delikatesas Joniškis (3–2).