Jiří Pernes (4 July 1948, Svitavy) is a Czech historian.
Between 1984-1990 he was director of the Historical Museum in Slavkov u Brna (Austerlitz), then between 1990-1992 he was director of the Moravské zemské muzeum in Brno. In 2011 he directed the Institute for the Study of Totalitarian Regimes. Jiří Pernes helds lectures at the Masaryk University in Brno and at the Jan Evangelista Purkyně University in Ústí nad Labem.
Nowadays he works in the Institute for Contemporary History at the Czech Academy of Science in Brno. He wrote many books and papers about Moravian, Czech and Czechoslovak history in 19th and 20th centuries.