The majority of the rural areas in developing countries are not connected to the electric grid. Rice production produces a significant amount of rice husk as a byproduct/waste but this waste can be used as a source of energy for drying of the rough rice. The aim of this research was to evaluate the performance and improve the design and operation of a rice husk fueled mixed flow grain dryer for small scale rural farmers using a validated 3-D computational fluid dynamics (CFD) model. The model was applied to predict the airflow and heat and mass transfer characteristics of the designed prototype rough rice dryer. The model took into account the geometrical detail of the dryer assembly, the relevant boundary and initial conditions, and model input parameters. The results identified relatively stagnant regions at the top and the side walls of the dryer. The observed relatively high variation in drying air velocity distribution caused a relatively high variation in drying characteristics of the rice grain. The model was applied to modify the design and operation procedure of the dryer to improve the performance in terms of drying uniformity and drying time. After 2 h drying time, the difference between the maximum and minimum moisture content values for the original and modified design was 12.9% and 8.5%, respectively. There was an exponential relationship between drying time and drying air temperature and specific flowrate. Mixing and recirculation of the grain at 30 min interval significantly improved the uniformity of drying, and the difference between maximum and minimum moisture content after 2 h of drying was clearly reduced to 1.9%. The study indicated the capability of 3-D CFD model to improve the design and operation of mixed flow rice husk fueled dryer to attain the required performance.