The effect of electron beam (EB) irradiation on the properties and compatibility of poly(ethylene 2,6-naphthalate) (PEN)/poly(ethylene terephthalate) (PET) blends was investigated. Upon EB irradiation, PEN/PET blends under-went transesterification reactions, resulting in the formation of more random copolymers from the original binary pair. The degree of transesterification increased with dose rate, and all of the irradiated blends exhibited a single glass transition temperature. This indicated that transesterification reactions promoted by EB irradiation led to the formation of a single phase. Transesterification reactions promoted by EB irradiation led to more random copolymers, and the reduced regularity in the irradiated blends decreased the melting temperature. A higher degree of randomness and lower number-average sequence lengths for the blend systems indicated that a more random chain structure was formed in the blends. The rheological measurements demonstrated that the irradiated PEN/PET blends were miscible. EB irradiation could promote transesterification reactions, thus enhancing the compatibility of PEN/PET blends.