Transesterification between poly-epsilon-caprolactone (PCL) and polyethylene-terephthalate (PET) under shear flow was investigated. Two types of flow were imposed to the test samples; one is a simple shear and the other is an oscillatory shear. Comparing to reaction at quiescent state, flow provides better conversion to the reaction. For simple shear flow, the rate of reaction increases as the shear rate increases, while under oscillatory flow, increasing the frequency and the amplitude enhances the extent of reaction. Improvements of the transesterification rate by simple shear prevail over those by the oscillatory motion. The results imply that the transesterification is mass transfer limited. The improvement of the reaction rate and the prevalence of the simple shear flow can be interpreted by the convective effect. The small margin between the rates of reaction under flow and at rest can be attributed to the small Reynolds number of the system.