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Due to critically inadequate capacity of roads, railways and ports, and inefficient transit procedures at borders and ports, transport costs are extremely high in Sub-Sahara African countries. This inefficient Cross-Border Transport Infrastructure (CBTI) system is considered to be the major bottleneck of industrial and economic development in the region, and thus should be improved for seamless cross-border trade and transport in order to promote regional development. Under the above assessments, this study targeted to propose: i) a development scenario of Sub-Sahara Africa with CBTI improvements, ii) a Japanese CBTI development strategy for Sub-Sahara Africa, and iii) a Japanese CBTI development program for East Africa (Uganda, Kenya and Tanzania), the model area of study, where a field survey was conducted. It was found that the major causes of lengthy transport time and high transport cost in the region were inefficient operation of ports and railways, and ineffective institutions and regulations on transit cargos. This finding has given an impact on Japan's subsequent CBTI development policy.