The non-Markovian master equation is applied to the calculation of reaction rates. Starting from the flux-side correlation function form, we treat both the thermal and real time evolution consistently within second order perturbation theory in the system-bath coupling. It is shown that the non-Markovian dynamics enter formally not only in the time propagation but also in the expressions for the initial system-bath correlations. We show that these initial correlations can have a significant effect on the reaction rate. The method presented, although approximate, is an effective way to calculate reaction rates for weakly coupled systems over a wide range of temperatures. As such it provides a complementary approach to the exact treatment based on the ML-MCTDH method of Craig et al. [1], which serves as reference in this work.