The hydrolysis of pectin with pectolytic enzymes is an extensively studied process, but its application for the clarification of glycosidic syrups produced from agro-industrial wastes is fairly limited. In this work, a model to simulate this process was proposed, considering the effects of the temperature, pH, stirring, inhibition, and enzymatic inactivation, relevant factors in this kind of processes. The kinetic parameters used in the model were estimated using the fmincon function from MATLAB by minimizing the global mean squared error. To validate the model, an experimental process was developed using a glucose syrup with an initial concentration of pectin of 0.05%, increasing the clarity from 65.75 to 88.1% after the application of the pectinase. The proposed model achieved a global mean squared error of 4.556%, lower than the threshold value of 10%, showing that the experimental data was successfully reproduced by the simulated data.