Zeitz was first recorded under the name Cici in the synode of Ravenna in 967. Between 965 and 982, it was the chief fortress of the March of Zeitz. Zeitz was a bishop's residence between 968 and 1028, when it was moved to Naumburg. Beginning at the end of the 13th century (1200s), the bishops again resided in their castle at Zeitz. The Herrmannsschacht (built in 1889) is one of the oldest brick factories in the world.
On 18 August 1976, the Protestant clergyman Oskar Brüsewitz from Rippicha burnt himself to death in front of the Michaeliskirche. This was a protest against the DDR system. The town was an industrial centre until German Reunification made many companies in eastern Germany uncompetitive. The town still has a large sugar factory.