FC Mika was originally founded as "Olimpia" in 1985. After the independence of Armenia the club was known as Kasakh Ashtarak. In 1999 it was renamed Mika by the owner of Armavia Airlines, Mikhail Baghdasarov. Under the merger, the name of the new club became Mika-Kasakh Ashtarak. However, the merger only lasted for one year, and in 2000, the two clubs separated. Kasakh Ashtarak kept its name, logo, history and statistics, while Mika settled for being a new club being known FC Mika Ashtarak.
In 2007, FC Mika relocated from Ashtarak to Yerevan. The club has already built its own stadium in the heart of Yerevan and uses it for domestic and European competitions. It has won 6 Armenian Cups and 1 Armenian Supercup since its foundation and is considered to be one of Armenia's top teams. As a Cup holder, Mika participated several times in UEFA Cup qualification matches, its best result being the second qualifying round in 2007, as the club passed MTK Budapest, but did not advance as it lost to Slovak club FC Artmedia.