The permeability of fractured rock mass is essentially governed by its geometrical characteristics, connectivity and filling materials of fractures, which commonly displays a significant correlation with the magnitude of the geostress field. Due to the limitations of existing models for the prediction of permeability, a novel empirical model (called ZRF model) is established to estimate the permeability coefficient of fractured rock mass by considering various factors. Particularly, the proposed model represents the permeability coefficient as a function of three geological indexes, i.e. buried depth (Z), rock quality designation (RQD) and filling substance designation (FSD). These three parameters are easily calibrated with packer hydraulic test data and borehole acoustic television images. Then the proposed model has been successfully applied to predict the permeability coefficient of fractured rock mass at the site of Yagen-II Hydropower Station and two other sites at which the borehole data are available in the literature. Advantages of the ZRF model include more clear physical significance and easy parameterization in engineering practices over the other existing permeability estimation models. The results indicate that the proposed ZRF model provides a feasible tool for the estimation of permeability of fractured rock mass at various field conditions.