Although there is evidence of some settlement in the region dating back to the Bronze Age, the true history of Travnik begins during the first few centuries AD. Dating from this time there are numerous indications of Roman settlement in the region, including graves, forts, the remains of various other structures, early Christian basilicas, etc. etc. In the city itself, there have been found Roman coins and plaques. Some writing found indicates the settlement is closely connected to the known Roman colony in modern day Zenica, 30 km away.

In the Middle Ages the Travnik area is known as the župa Lašva province of the medieval Bosnian kingdom. The area is first mentioned by Bela IV of Hungary in 1244. Travnik itself was one of a number of fortified towns in the region, with its fortress Kaštel becoming today's old town sector. The city itself is first mentioned by the Ottomans during their conquest of nearby Jajce.

Vizier's grave(turbe) in Travnik

Following the Ottoman conquest of Bosnia, much of the local population converted to Islam. The city quickly grew into one of the more important settlements in the region, as authorities constructed mosques, marketplaces, and various infrastructure. In 1699 when Sarajevo was set on fire by Field-Marshall Prince Eugene of Savoy, Travnik became the capital of the Ottoman province of Bosnia and seat of the Bosnian viziers. This period is generally thought of as Travnik's golden age. The city became an important center of government in the whole Western frontier of the empire, and consulates were established by France and Austria-Hungary, leading some to label it, "The Bosnian Istanbul".

The period of Austrian occupation brought westernization and industry to Travnik, but also a heavy decline in importance. While cities such as Banja Luka, Sarajevo, Tuzla, and Zenica grew rapidly, Travnik stayed behind so much that in 1991 it had a mere 30,000 or so people, with 70,000 in the entire municipality.

During the Yugoslav Wars, the city escaped most of the damage from Serb attacks. Following this, conflict arose between the area's Bosniaks and Croats, which has led some to accuse the Bosnian army of ethnic cleansing. Following the war, Travnik was made the center of the Central Bosnia Canton.