Biodiesel is assumed a renewable and environmentally friendly fuel that possesses the potential to substitute petroleum diesel. The basic purpose of the present study is to design a precise algorithm based on Gaussian Process Regression (GPR) model with several kernel functions, i.e., Rational Quadratic, Squared Exponential, Matern, and Exponential, to estimate biodiesel properties. These properties include kinematic viscosity (KV), pour point (PP), iodine value (IV), and cloud point (CP) as a function of fatty acid composition. In order to develop this model, some variables are assumed, such as molecular weight, carbon number, double bond numbers, monounsaturated fatty acids, polyunsaturated fatty acid, weight percent of saturated acid, and temperature. The performance and efficiency of the GPR model are measured through several statistical criteria and the results are summarized in root mean square error (RMSE) and coefficients of determination ( R 2 ). R 2 and RMSE are sorted as 0.992 & 0.15697, 0.998 & 0.96580, 0.966 & 1.38659, and 0.968 & 1.56068 for four properties such as KV, IV, CP, and PP, respectively. It is worth to mention this point that the kernel function Squared Exponential shows a great performance for IV and PP and kernel functions Exponential and Matern indicate appropriate efficiency for CP and KV properties, respectively. On the other hand, the results of the offered GPR models are compared with those of the previous models, LSSVM-PSO and ANFIS. The outcomes proved the superiority of this model over two former models in point of estimating the biodiesel properties.