In this study, four Gaussian process regression (GPR) approaches by various kernel functions have been proposed for the estimation of biodiesel density as the functions of pressure, temperature, molecular weight, and the normal melting point of fatty acid esters. Comparing the actual values with GPR outputs shows that these approaches have good accuracy, but the performance of the rational quadratic GPR model is better than others. In this GPR model, RMSE = 0.47, MSE = 0.22, MRE = 0.04, R2 = 1, and STD is equal to 0.3. In addition, for the first time, this study shows that the effective parameters affect the biodiesel density. According to this analysis, it was shown that among the input parameters, pressure has the greatest effect on the target values with a relevancy factor of 0.59. This study can be used as a suitable and valuable work/tool for chemical and petroleum engineers who attempt environment protection and recovery improvement.