For Africa's developing countries the agricultural system is among the most vulnerable due to extensive use of rainfed crop production, presence of droughts and floods that affect crops as well as initial poverty of population that limits the capacity to adapt. In this study were realized the analysis of long-term rainfall data and its impact on main crop products in Rwanda. Some rainfall data was infilled for the period of 1926-2013. It was done using the monitoring data of a neighbor weather station with relatively the same elevation above sea level and with a monitoring record of no less than 40 years. The neighboring station with the best correlation was selected for the infilling. The missing rainfall data was infilled for all the stations with resulting regression coefficients ranging from 0.55 to 0.80. This indicates the acceptability of the performed regression. Also were constructed different-cumulative curves of rainfall and sort out cycles of decline and increment of rainfall. Similar different-cumulative curves were constructed for main crops in Rwanda. Correlation and regression analysis were used to determine the relationship between rainfall, arable land expansion, fertilizer use and crop yield. Particularly for Rwandan conditions, the rainfall variations are determinant for the crop yield increment. The intensification of extreme flood's and, as rule, flooding of agricultural lands in connection with rainfall augmentation was also allocated.