The Comprehensive Peace Agreement (CPA), which was signed by the government of Sudan and the Sudanese People’s Liberation Movement (SPLM) ended more than 20 years of civil war. According to the CPA, the Sudan’s government has 50% of the oil exploited from the wells existing in the south in addition to the oil produced from the northern wells. The latter represents about 30% of the total oil production in Sudan. In January 2011, the people in southern Sudan have voted for separation from the Sudan and in July 2011 the Republic of South Sudan was officially announced as Africa’s newest state. Now the CPA period is over and the south possesses its entire production of oil, but need to use the export infrastructure that exists in the north to export it. For that the south need to pay fees and customs for which the exact amounts need to be further negotiated. Sudan would lose a huge part of its revenue from oil, which constituted a growing share in its trade, government revenue and GDP during the last decade. This paper tries to investigate the consequences of separation on the Sudan’s economy. A regional general equilibrium model with Africa database of the Global Trade Analysis Project (GTAP) is applied. Results show that the entire economy would be hit when a 20% cut in oil output is simulated. The study introduces the non-oil exports of the agricultural sector as an alternative to oil and recommends enhancing the efficiency in agriculture and promoting agricultural exports to gradually bring the economy back on track.