The sub-prefectures of the department are Bégbessou, Bouaflé, N'Douffoukankro, Pakouabo, and Tibéita.
Using current boundaries as a reference, the department occupied the same territory that is today Marahoué Region.
Bouaflé Department was included as part of Marahoué Region.
In 2011, districts were introduced as new first-level subdivisions of Ivory Coast.
At this time, Bouaflé Department remained part of the retained Marahoué Region in the new Sassandra-Marahoué District.