An improved non‐isothermal kinetic model was developed based on mass balance and Arrhenius laws using a second‐order reversible reaction capable of predicting the extent of transesterification reaction (X) and the degree of randomness (RD) in poly(ethylene terephthalate) (PET)/poly(ethylene naphthalene‐2,6‐dicarboxylate) (PEN) blends prepared by a twin screw micro‐compounder over a full composition range under different processing conditions. The experimental values of X and RD were determined by 1H‐NMR and a direct relationship between them developed. The model constants were tuned by an optimization method using half of the experimental data, with the other half used for verification. Good agreement was found between the experimental and theoretical data in the verification stage and, therefore, it was concluded that the model is capable of predicting the extent of transesterification reaction with a high level of confidence for a wide range of processing conditions. Similarly to the experimental results, the model showed that, among all parameters affecting the extent of transesterification reaction, the time and temperature play the major role, whereas the blend composition does not have a significant role.magnified image