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The performance of livestock marketing system in South Sudan is not well understood, though livestock is the only significant agricultural commodity on the market in South Sudan, and also despite the great social and economic importance of livestock for South Sudan's rural and urban populations. There are uncertainties over whether the Comprehensive Peace Agreement (CPA) that was signed in 2005 has had a significant effect on the cattle market performance. There was thus a need to assess the trends in the cattle market performance in South Sudan during and after the civil conflict in Sudan by comparing the trends in the marketing margins for different marketing agents through descriptive analysis and by assessing the effect of marketing costs on marketing margins for the different market actors through regression techniques. In this regard, the study used the Fixed Effects model utilizing Panel Data and analytical approaches based on the farm value, wholesale-to-retail margins, and farm-to-retail price spread.