Central Equatoria, like other states in South Sudan, was sub-divided into counties which are further divided into Payams, then Bomas.
Important cities and towns of Central Equatoria were: Juba, Kajo Keji, Liria, Mongilla,Wonduruba, South Sudan Wonduruba, Rokon, Tali, Terkeke, Yei, Ji-Meje, Tombek, Tindilo, Kaya, Muni and Rijong, Bubudo(Nyori).