The football team played in Antra Lyga (3rd tier) and had no desire to move up to a higher division.

In the beginning of 2004, a new organization called VšĮ „Šiaulių futbolo klubas“ was established.

Its leaders sought to build a strong, winning team to rise to A Lyga (top tier).

The 2012–13 UEFA Europa League lost to FC Levadia Tallinn (2–2 aggr.)

In 2015 the team faced serious financial problems and did not pay their players proper salaries.