A semibatch melt prepolymerization of poly(ethylene terephthalate) (PET) is studied. Being characterized by complex reaction pathways leading to various functional end groups and side products, PET prepolymerization process poses a challenging modeling problem. Ten distinct polymeric species have been defined in accordance with the type of functional end groups and the corresponding mass balance and moment equation are developed to estimate the progress of reaction and polymer molecular weight. The effect of various reactor operating conditions on the performance of the polymerization process has been examined through numerical simulation of the molecular species model developed. In particular, the effect of incomplete transesterification of methyl ester groups on the polymer molecular weight has been investigated in detail.