After concluding the Comprehensive Peace Agreement (CPA), the Central Bank of Sudan Act 2002 was amended in 2006, wherein the nature of the banking system, the Bank and its branches, were specified in Section (5) from the Act as follows:

1. The Sudanese banking system shall consist of dual banking system; one of which is Islamic, in Northern Sudan, and the other Conventional, in Southern Sudan.
2. The headquarters of the Bank shall be in Khartoum, and may establish branches , or agencies inside the Sudan, and appoint correspondents outside the Sudan.
3. The Bank of Southern Sudan shall be established as a branch of the Bank to render, in addition to its other tasks, conventional banking services, in Southern Sudan, including the issue of license, as the Board may issue. There shall assume management of the conventional banking system, in Southern Sudan, as one of the windows of the Bank, and in accordance with its laws, policies and safeguards.
4. The Bank shall have an independent corporate personality, perpetual succession, a common seal, and the right to litigate , in its power name.

After the secession of Southern Sudan, the Bank of Southern Sudan (BOSS) became the central bank of the State of Southern Sudan on the 9^th of July 2011. All branches of Central Bank of Sudan in the previously southern states became affiliated to it. Topics related to Item no (14) of the Protocol of wealth sharing, concerning the monetary policy, banking, currency, and lending has been frozen. In addition to this,  policies of the traditional banking system in southern Sudan,  and all circulars of the Central Bank of Sudan related to the dual system has been suspended, until the amendment of the law of the Central Bank of Sudan for the year 2002.