The oldest historical records to mention Kopčany date from 1392. However, the village is much older. In the 9th century, Kopčany was part of the agglomeration of Mikulčice, an important center and possibly the capital of Great Moravia.
Kopčany is also the site of one of the oldest standing buildings for which a Great Moravian origin is postulated, the Church of St Margaret of Antioch.