Diesel fuel is a significant energy source in automobiles, but the way diesel fuel pollutes the environment is alarming. There is an urgent need for fuel which produces the least pollution to the environment and renewable sources. In this paper, a single-cylinder, water-cooled, common rail direct injection diesel engine was run with jojoba biodiesel by changing input parameters, i.e., blend% (10, 15, 20, 25, and 30), load (0, 3, 6, 9, and 12 kg), compression ratio (16, 17, 18, 19, and 20), and injection pressure (190, 210, 230, 250, and 270 bar) to maximize the performance parameters, i.e., brake thermal efficiency, brake power, brake-specific fuel consumption, and exhaust gas temperature, also to minimize emission, i.e., carbon monoxide, unburnt hydrocarbon, NOx (oxides of nitrogen), and smoke. MINITAB20 software was used to display the results and graphs. The result shows a significant decrease in all emission variables except a marginal increase in NOx emission. Performance parameters show a slight decline in value compared to pure diesel fuel. The results reveal that the overall good performance of the engine with brake thermal efficiency leads to a maximum value of 24.5%. Brake power was found to be a maximum value of 4.4 kW. The brake-specific fuel consumption minimum value was found to be 495 g/kWh, and the exhaust gas temperature result shows the minimum temperature of 181 ℃. The value of emission parameters such as carbon monoxide, unburnt hydrocarbon, NOx, and smoke was 0.11% Vol., 11 ppm, 250 ppm, and 8 HSU, respectively, with their respective configurations. The optimum value of the output variables, analyzed by Response Surface Methodology, is at a blend of 10.2020%, IP 190 bar, CR 20, and load 2.7879 kg. The desirability of this experiment is 78.82%, as analyzed by Response Surface Methodology.