[5]: 299  The town was founded by Soninke Wangara merchants (the ancestors of the Dyula people) in the mid 18th century shortly before or immediately following the destruction of Bighu at the hands of the Ashanti Empire.

"[7][5]: 297 Originally a Dyula trading center, Bondoukou was conquered by the Abron, an Akan people, in the early seventeenth century; it soon became the economic hub of the Gyaaman kingdom.

[8] On 13 November 1888, the French officer Treich-Laplène signed a Protectorate treaty with the Abron king of Bondoukou, but the city fell to Samori between September 1895 and July 1897.

In 1964 Boundoukou was made administrative center for its region, and as since regained its status, and is the seat of the Prefect governing Bouna, Tanda, and Bondoukou Departments.

On the dividing line between government and rebel zones of control during the Ivorian Civil War, Bondoukou became the main north-eastern base of the United Nations Operation in Côte d'Ivoire (ONUCI).

The walled old city (Medina) includes ethnic neighbourhoods from far flung groups who originally came to the area as part of long distance trade networks.

Outside the town, historic sites include an Akan ceremonial center at Soko (just east), pottery works at Montiamo, the treasure house of the Abron war-leader at Wéletchéi (just north), and the French colonial era plantations at Goli (just west).

The town is home to several schools (from primary to post-secondary), a regional hospital and an Ivorian second division Football club, Scaraboutou sports de Bondoukou.