Diesel engines have considered as the popular internal combustion engine used in transport, agriculture-forestry-fishery, and power generator due to their utility. Stringent norms of the environment, increasing demand of energy, and depleted fossil fuel have led to looking for an alternative and renewable energy source. Jatropha oil-based fuels were considered as the appropriate energy source in the future to replace traditional diesel fuel. However, some problems such as coke and deposit formation resulting in the changes in fuel spray characteristics and engine performance were encountered because of high kinematic viscosity and density of straight Jatropha oil when used for diesel engines. The aim of this study is to improve the drawbacks of Jatropha oil by heating before being fueled a 4-stroke-4-cylinder diesel engine. The deposit formation around the injector tips, fuel spray characteristics (including penetration length and cone angle), combustion, and emissions of the above-mentioned diesel engine running on preheated Jatropha oil and diesel fuel after 300 h were practically measured and compared to the first hour (0 h). After completion of the long-term 300 h test, some results of the test engine fueled with preheated Jatropha oil such as a huge amount of deposits around the injectors tips resulting in partly clogging the nozzle holes and increasing penetration length to 10.52%, a decrease of 30.73% for engine power and 7.28% for NOx emissions, an increase in 8.63% of HC and 6.96% of CO emissions were detected; meanwhile, the above parameters for diesel fuel after 300 h of test were insignificantly different from the first hour. Moreover, the element components in deposits were also thoroughly analyzed by EDS, and optical observation was assisted by SEM.