Originally was established as a football team of the Black Sea Shipyard, since dissolution of the Soviet Union and cutting of the shipyard's budget which was based mostly on military contacts, it is sponsored mostly by the city of Mykolaiv.

It is the oldest continuously playing club in the country that competes on the professional level.

Throughout the Soviet times and until the 1990s, it mostly played under the name of Sudnobudivnyk meaning Shipbuilder associated with the Black Sea Shipyard.

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.