The first written record of Chotěboř dates back to 1265. At that time, Chotěboř was one of the mining areas owned by Smil of Lichtenburg. Around 1329, the King of Bohemia, John of Luxemburg, purchased the town, and in 1331, Chotěboř was granted a royal charter. Charles IV, King of Bohemia and Holy Roman Emperor, further expanded the charter, bestowing upon the town a seal exactly the same as the crest of Bohemia itself (a silver lion on a red field). Walls were built around the town, and the fortifications were completed in 1391. 
Chotěboř entered into the history of the Hussite Wars inauspiciously in 1421, when Táborite Prince Peter Hromadka of Jistebnice captured the town and became the town Hetman (military governor). The Hussites under Hromadka leadership, however, later had to surrender to the superior numbers of Catholic forces. Although the victors initially granted the vanquished free passage out of the town, they drove them into three barns, where they burned 300 hostages to death. Hromadka himself was executed in the city of Chrudim , 40 km north of Chotěboř.
At the end of the 15th century, Chotěboř fell to the family of Trčků z Lípy, and the area saw a flourishing of artisans. During the Thirty Years War (1618-1648), the Trčků z Lípy family sided with Albrecht of Waldstein and thus fell out of favour with Hapsburg Emperor Ferdinand II (ruled 1620-1637). Its property was confiscated. 
From 1636 onward, Chotěboř and the Chotěboř estate were associated with a series of owners, the final one being the Dobřenský family (1841-1948). In 1948, the estate was confiscated by the state, but it was returned to the Dobřenský family in 1992.
Toward the end of the 19th century, Chotěboř began to see the growth of industry. The key to this development was the building of the railway line through the town, connecting Německý Brod (today Havlíčkův Brod) to the south with Rosice nad Labem to the north. The first train went through Chotěboř in 1871.