Metalurh takes its roots from the Football Club Prometei Shakhtarsk that was allowed to participate on the non-amateur level once Ukraine attained its independence. After a disappointing first season in the Second League, in the 1993 season Promotei placed fifth in the Third League and was promoted back to the Second League when the third place Antratsyt withdrew from competitions. Due to being sponsored by a Medita health clinic of Oleksandr Opryshchenko, in 1993 the club was renamed as Medita Shakhtarsk. However in 1995 the club's owner was killed and Promotei returned under ownership of the state coal-mining company "Shakhtarantratsyt" under the name of Shakhtar Shakhtarsk.
In 1996 a team of the Donetsk Metallurgical Factory replaced the insolvent FC Shakhtar Shakhtarsk during the 1995-96 season under the name of Shakhtar. In summer of 1996 the Donetsk Regional Football Federation agreed to handover the Shakhtar's past season achievements to the newly formed and already widely accepted, Football Club Metalurh Donetsk. After placing second in the Druha Liha Group C, the club gained the promotion to the Persha Liha. In the next season, 1996–97, Metalurh won the Persha Liha championship and were promoted to the Vyscha Liha.
The club successfully started in the Top League and also improved significantly at the domestic Cup competition. Metalurh has managed to obtain few bronze medals in the League and since 1998 made through to at least the quarter-finals of the Ukrainian Cup. The club financially struggled between 1999 and 2001 being kept afloat by individual efforts of Mykhailo Lyashko and Vladyslav Helzin who both in 2001 decided to created their own club (see FC Olimpik Donetsk).
In 2001 Metalurh was purchased by ISD, Ukrainian industrial corporation owned by Serhiy Taruta, one of the most wealthy businessmen in Ukraine and Europe. Throughout majority of the first decade of the new millennium, Metalurh's owners developed a close working relationship with well-known Ukrainian agent Dmytro Sylyuk, who soon became club's acting chairman and has gained a lot of bad publicity for bringing numerous foreign players into the club. Also, while working with Metalurh, Selyuk has lived in Barcelona and was a rare visitor to Ukraine. For several seasons, the foreigners, Selyuk's clients, have outnumbered domestic players. Many of the signed players were brought in without manager's consent, and a lot have been given an overly generous pay; among those were Yaya Touré, Andrés Mendoza, and Jordi Cruyff. After Sylyuk's questionable tactics, he was dismissed from his position and majority of the players brought in by him also left. As it appeared later, many of them have had contracts with Sylyuk, and not directly with the club.
After the era of Sylyuk ended, Metalurh's performance declined and a hunt for medals turned into a struggle for survival. However, in 2008, Bulgarian specialist Nikolay Kostov was brought in to rebuild the team. In his first season with the club, Kostov turned Metalurh's performance around and the club came fourth in the league, which granted them a spot in newly formed UEFA Europa League.
Metalurh has its own small stadium named after the club, Metalurh Stadium. For most domestic matches the club plays at this stadium, which has a capacity barely in excess of 5,000. For games expected to draw a significantly larger crowd, Metalurh plays at Shakhtar Stadium, owned by Shakhtar Donetsk. The Shakhtar Stadium is mostly used for the European competitions. A new stadium for Metalurh with a capacity of 17,500 is under construction in Makiivka, near Donetsk.
The club are currently playing their home games at Obolon Arena in Kiev due to safety concerns in Donbass.
Metalurh's top rivals are the neighbor club and one of Ukraine's most successful teams, Shakhtar Donetsk. The two clubs have not only had a close history since formation of Metalurh, but the club has also played at Shakhtar's former venue, Shakhtar Stadium. The games between the two clubs have been dubbed by the fans and the media as Donbass Derby, although Shakhtar has been dominant in the rivalry for a decade from 1996 and up until 2006, winning all 18 games between them, matches between the two have always been of a major significance to fans.