Abstract: Seismic isolation is an effective technology to improve seismic resilience of buildings. The function of flexible pipes with a large deformation requirement in the isolation layer is critical, but the fragility model and consequence functions of such pipes were rarely reported, which hinders the seismic resilience assessment of isolated structures. To address this issue, this paper took rubber flexible pipes as examples, identified two critical damage states based on previous experiments. Then, the seismic fragility models of flexible pipes with nominal inner diameters of 50 mm and 100 mm were established. The corresponding consequence function of repair cost was recommended with the consideration of different costs, while the corresponding consequence function of repair time was proposed according to the data of disassembly and installation time of 24 specimens. Subsequently, the developed fragility models and consequence functions were applied to evaluate the seismic resilience of a five-story isolated RC frame structure under design earthquake and maximum considered earthquake respectively, in which six design schemes of flexible pipes were considered with emphasis put on different nominal inner diameter and design length. The results indicate that under design earthquake and maximum considered earthquake, the repair cost of flexible pipes can be up to 88.5% and 29.4%, while the influence of corresponding repair time is negligible. The repair cost of such pipes under design earthquake can be significantly reduced through the increase of design length. In contrast, due to the large deformation under maximum considered earthquake, the increase of design length cannot prevent the pipes from failure if the length is smaller than that regulated in the code, leading to an increase of repair cost. The research outcome can provide an important reference for the seismic resilience assessment and design of isolated buildings.