The technical, allocative and economic efficiency in soybean production among small-holders in Benishangul-Gumuz region was estimated using the stochastic frontier production function analysis. The main objective of the study was to explore ways likely to increase productivity of soybean among small-holder farmers in the region through a better use of the factors employed in soybean production. The study were used primary data collected from a sample of 266 soybean producer farmers of Assosa and Bambasi districts through administration of structured questionnaire. Multi-stage random sampling technique was employed to select sample respondents. The respondents were randomly selected from nine villages of the two districts where the scaling-up of soybean technologies being introduced. Descriptive statistics were used to analyze socioeconomic characteristics while the stochastic frontier production function was used, in order to estimate the level of technical, allocative and economic efficiencies among sample farmers. The results further revealed the existence of inefficiencies in soybean production among farmers in the study area. The mean technical efficiency of soybean producer farmers was found to be 72.81% while the average efficiency of allocative and economic were 55.13% and 40.08%, respectively. On the determinants of inefficiency, the study found that educational level, farming experience, distance to cooperative and input center significantly reduce the technical inefficiencies among soybean farmers, whereas distance to main road, access to credit, frequency of extension contacts, farming experience and ownerships to tropical livestock unit decreases allocative inefficiency of soybean among producers. On the other hand, educational level, frequency of extension contact, experience in farming, distance to cooperative and input center significantly reduce economic inefficiencies among soybean producer farmers in study area. The result emphasize the need for building rural infrastructure, adult education and training of farmers in FTC and demonstration new technologies, institutional support of credit services and increasing frequency of extension and improving livestock health and nutritional improvements in the study area.