In today’s scenario, biodiesel is one of the best alternatives to diesel for application as an eco-friendly product. In this work, jojoba oil is transesterified using solar energy for heating purposes. A solar parabolic trough collector having 6.4 m2 and 89% reflectivity is used to concentrate solar rays on a sealed container containing jojoba oil and catalyst-alcohol mixture, placed at the focus of the dish. The performance parameters like molar ratio (MR), reaction time (RT), and catalyst concentration (CC) are optimized. The result showed the highest yield of 89.67% at the optimum condition of molar ratio 9:1, reaction time 120 min, and catalyst concentration 0.8 wt.%. The highest contribution of 55.13% is measured for the molar ratio, followed by reaction time and catalyst concentration. Later, the interaction between MR, RT, and CC is established by response surface/contour plots; and their effects on biodiesel yield are discussed. Subsequently, the various physicochemical properties of raw jojoba oil and jojoba oil methyl ester are also measured and discussed as per ASTM standards. The unsaturated acid content in the biodiesel is also measured by gas chromatography. Hence, the blends of linseed oil with diesel fuel can be used in the IC engines with little or no modifications in engine parameters. Therefore, the use of solar energy could effectively reduce the use of electricity to cut down the processing cost in biodiesel production. Also, the methods should be established for methanol recovery from glycerine.