Yes / Batch oxidative desulfurization (ODS) process is investigated here for the removal sulfur compound from light naphtha using homemade new nano-catalyst. The catalyst is made of manganese dioxide supported on zeolite nanoparticles which shows an excellent catalytic performance with good impregnation, high activity, good pore size distribution and larger surface area. Different reaction temperature, time and initial sulfur concentration are used to have a deeper insight of the process. The experimental results reveal that the conversion of sulfur compound is increased by increasing the initial sulfur concentration, the reaction temperature and batch time. A mathematical model of the process is developed and validated using the experimental data within gPROMS software with high accuracy. The validated model (errors less than 5% between experimental and predicted results) is then utilized to obtain the optimal operation conditions of the process giving maximum conversion of sulfur (higher than 99%) resulting in an environmentally friendly fuel.