The study examined the gender difference and its impact on agricultural productivity in Sheko district of Bench Maji zone, located at 573 km south west of Addis Ababa, the capital of the country. The specific objectives were to assess the extent to which the agricultural production system is gender oriented; to examine access and control over productive resources; and to estimate men’s and women’s productivity in agriculture. Cross-sectional data collected from a total of 150 respondents were used in this study whereby 75 were female headed and 75 were male headed households. The data were analyzed using Statistical Package for Social Science (SPSS). Descriptive statistics such as frequency, mean, percentage, t-test and chi-square were used to summarize and compare the information between the two groups. Moreover, Cobb-Douglas (CD) production function was used to estimate the productivity difference in agriculture between male and female headed households. Results of the study showed that male headed household s (MHH) own more of productive resources such as land, livestock, labour and other agricultural inputs as compared to female headed households (FHH). Moreover, the estimate of CD production function shows that livestock, herbicide use, land size and male labour were statistically significant for MHH while livestock, land size, herbicides use and female labour were significant variables for FHH. The comparison of the marginal value product (MVP) with the factor cost showed that MHH could increase productivity using more herbicides and male labour while FHH could do so by using more herbicides, male and female labour. The agricultural productivity difference between MHH and FHH was about 66.76% in the study area. However, if FHH had equal access to the inputs as MHH, gross value of the output would be higher by 21.39% for FHH. This may suggest that FHH would be more productive than MHH if they had equal access to inputs as MHH. Based on the results obtained, the following policy implication can be drawn: accessing FHH to inputs that increase the productivity of agriculture such as herbicides, livestock and male labour; increasing the productivity of land; and introducing technologies that reduce the time and energy of women.