The sub-prefectures of the department are Appimandoum, Bondo, Bondoukou, Gouméré, Laoudi-Ba, Pinda-Boroko, Sapli-Sépingo, Sorobango, Tabagne, Tagadi, Taoudi, and Yézimala.

Using current boundaries as a reference, from 1969 to 1974 the department occupied the same territory that is today Zanzan District.

[4] From 1974 to 1988, Bondoukou Department occupied the same territory that is today Gontougo Region.

[4] In 2011, districts were introduced as new first-level subdivisions of Ivory Coast.

At this time, Boundoukou Department became part of Gontougo Region in Zanzan District.