Bongouanou Department was created in 1980 as a split-off from Dimbokro Department.[3] Using current boundaries as a reference, from 1980 to 2009 the department occupied the same territory as Moronou Region.
In 1997, regions were introduced as new first-level subdivisions of Ivory Coast; as a result, all departments were converted into second-level subdivisions. Bongouanou Department was included in N'Zi-Comoé Region.
In 2011, districts were introduced as new first-level subdivisions of Ivory Coast. At the same time, regions were reorganised and became second-level subdivisions and all departments were converted into third-level subdivisions. At this time, Bongouanou Department became part of N'Zi Region in Lacs District. In 2012, it was joined with Arrah and M'Batto Departments to form the new Moronou Region.