An experimental method to measure the reduced stiffness of the fatigue loaded polymer concrete was developed. Fatigue testing of the concrete was performed by applying a periodic load in bending tests. To investigate the reduction of stiffness due to fatigue damage, the frequency dependent variations of the dynamic stiffness and loss factor of the polymer concretes (a mixture of epoxy resin, carbon fiber, and aggregates) were obtained by impact tests. The variations of the dynamic properties before and after the fatigue tests were measured. The separated beam method was used to identify the stiffness distribution along the concrete specimens. This method analyzes the beam vibration using evenly spaced beam elements. The boundary conditions of displacement and slope continuity at the ends of each element were imposed. The least square method was applied to estimate the dynamic properties of the beam elements from the measured vibration responses. This procedure was required to identify small changes of the dynamic properties induced during the fatigue tests. Consequently, the durability of the carbon fiber reinforced polymer concretes was validated by comparison with normal polymer concretes.