Abstract There is a rapid increase in the air pollution level of the earth atmosphere due to the extreme demand and usage of the petroleum products. The demand has accelerated the recent research to explore an environment-friendly fuels suitable for the performance on the diesel engine. The optimization of the engine parameters using RSM with combination of taguchi method is an important aspect which generates an important optimized model for the responses. In the present study, an investigation of optimum performance and emission parameters of an engine fuelled with jojoba biodiesel is presented. The study also includes the optimization of input parameters to attain corresponding optimal thermal performance of the engine. The input parameters are injection pressure, injection timing of fuel, percentage blends of jojoba based biodiesel and engine load whereas the corresponding output responses such as brake thermal efficiency, peak cylinder pressure, exhaust gas temperature, and hydrocarbon emission are considered for the optimization during the investigation. The experimental design used in the study is based on a central composite rotating design matrix. The best combination of input parameters is recorded at 25°bTDC injection timing of fuel, 21.52 MPa injection pressure of fuel, 24% mixing of jojoba biodiesel with diesel, and 80% engine load which maximum BTE and Pmax minimum EGT and UHC emission of the engine. Experimental and optimized results of the output responses at optimum input parameters are compared and they were found to be in the suggested error range.