This paper develops a two warehouse inventory model for non-instantaneous deteriorating items with partial backlogging and stock-dependent demand. In the model, shortages are allowed and the backlogging rate is variable and dependent on the waiting time for the next replenishment. The necessary and sufficient conditions of the existence and uniqueness of the optimal solution are shown. Numerical example is presented to demonstrate the developed model, followed by the sensitivity analysis of the optimal solution with respect to key parameters of the inventory system. The purpose of this study is to determine the optimal replenishment policy by minimizing the total optimal cost. The proposed model can assist a decision maker in making important replenishment decisions.