In the beginning of this Diocese, it was first named as Kapoeta Archdeaconry under the leadership of Ven. Isaac Deu Chol as the first Archdeacon of Kapoeta Archdeaconry in 2008. And in the beginning of 2012, it was divided into three (3) Archdeaconries namely:

• Kapoeta Archdeaconry headed by Ven. Gabriel Amol Garang as Archdeacon of Kapoeta Archdeaconry.
• New Site Archdeaconry headed by Ven. David Deng Garnag as Archdeacon of New Site Archdeaconry.
• Narus Archdeaconry headed by Ven. Abraham Guor Ganag as Archdeacon of Narus Archdeaconry.

And in the same procedures, Ven. Isaac Deu Chol was promoted to be Commissary of the Diocese of Torit and in the same time as the secretary of Proposed Area of Kapoeta under Torit” Diocese.
In year 2013 the synod set under the leadership of His Lordship Rt. Rev. Bern, Bishop of Diocese of Torit and passed the approval of Kapoeta Area Diocese in Magwi in February 2013.
On the 3rd day of May, 2015, Rt.Rev.Isaac Deu Chol was consecrated as the Assistance Bishop of Kapoeta Area Diocese under Diocese of Torit.
On the 2nd day of April 2017, Bishop Isaac Deu Chol was enthroned as the first Bishop of Diocese of Kapoeta at St. Matthew Cathedral which authorized him to be missionary Bishop.