This study was carried out to establish farmers’ perceptions regarding low agricultural productivity and to document their proposals for improving the performance of agriculture sector in South Sudan. The results reveal that the major challenges related to low agricultural productivity as perceived by farmers include poor leveling of fields, poor irrigation management, low water availability, loss of land due to salinity and low water use efficiency due to seepage and runoff losses. Low water availability is considered as the biggest challenge for improving agricultural productivity because dependence on seasonal rain results in low crop yields and serious food shortages during most part of a year. Therefore, installation of public wells to increase groundwater availability for irrigation and establishment of rainwater harvesting structures are proposed as the potential solutions to solve irrigation water problems and overcome food shortages. Strengthening of extension services and training of vegetable growers on drip and sprinkler irrigation system along with the provision of irrigation equipment can help a great deal in increasing agricultural productivity. The state and national governments should provide high quality seeds and loans to the vegetable growers to enable them improve their crop production and cultivation of crops during the dry periods.