The club was originally founded in 1920 under the name Sudostroitel (Sudnobudivnyk) Mykolaiv and it is the oldest continuously playing club in the country that competes on the professional level (superseding even Dynamo Kyiv). Holding this record the club never attained any real triumphs and was always competing in the lower divisions. Throughout the Soviet times and until 1990s it always played under the name of Sudnobudivnyk. MFC Mykolaiv took part in the first Ukrainian Premier League season in 1992 under the name FC Evis Mykolaiv, after being initially chosen to participate for being one of the top 9 (of 11) Ukrainian teams from the West Division of the Soviet Second League 1991. The club is one of the holders of the unfortunate distinction as being the team to be demoted three times from the Ukrainian Premier League.
MFС Mykolaiv's best achievement in the Ukrainian Premier League was 13th place (in 1994–95). From 1994, the club was known as SC Mykolaiv, FC Mykolaiv since 2000, and MFC Mykolaiv since 2006.
MFC Mykolaiv became insolvent and ceased to exist after the City Administration of Mykolaiv informed the PFL that the team would not be competing in the 2008/09 Persha Liha season. The team then requested re-admittance to the PFL, but it was too late as the calendar was already set up. The PFL allowed the club to compete in the Druha Liha, but only in the next season. The administration of the FC Dynamo Kyiv extended its helping hand by withdrawing its junior team Dynamo-3 from the Second League and, thus, for Mykolaiv to be placed instead of it.
Squad is given according to the Ukrainian Football League official website. Note: Flags indicate national team as has been defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.
^Club announced dissolvement 2 July 2008. PFL proceeded to remove the club from the professional ranks. The club under pressure from local civil sources reapplies and the PFL grants the club reinstatement in the Druha Liha Group A for the 2008–09 season at the expense of FC Dynamo-3 Kyiv who withdrew to allow the League to have 18 teams.