With the rapid development of energy-based seismic design, probabilistic seismic hazard analysis (PSHA) in terms of the input energy spectrum, E I, has become increasingly important. Generally, implementing E I-based PSHA requires a ground-motion prediction equation (GMPE) for E I. However, although a GMPE for E I can be constructed in regions with abundant earthquake data based on regression analyses, it is difficult to obtain in regions lacking strong ground-motion records. Therefore, this study proposes a new approach for performing E I-based PSHA in regions with limited earthquake data. Instead of using a GMPE for E I directly, a model of Fourier amplitude spectrum (FAS) is adopted, which can be determined using a small number of earthquake data with small-to-moderate magnitudes. Then, the E I of the ground motion is obtained from FAS based on the relationship between E I and FAS. Furthermore, to calculate the annual intensity exceedance rate within the proposed framework of adopting the FAS model, a highly efficient method, namely, the moment method, is applied. Several numerical examples indicate that the proposed approach not only is suitable for regions lacking strong ground-motion records but also performs very efficiently in calculating the annual intensity exceedance rate.