This paper provides a new methodology for seismic performance evaluation and retrofitting of structures using the combination of fault tree and incremental dynamic analysis to cover some of the limitation of the existing methods. These limitations include the qualitative consideration of performance objectives, the consideration of uncertainties, and the lack of a systematic method for determining the retrofitting strategy. In this method, first, the fault tree model of the structure's intended performance is drawn, considering possible failure modes. Then, using incremental dynamic analysis, the seismic fragility curves for all failure modes are derived. In the next step, having these fragility curves and using the fault tree analysis of the structure, the fragility curve of the whole structure is determined. By integrating the fragility curve of the structure and the seismic hazard curve of the site, the intended performance risk is calculated. This risk is a quantitative performance goal that can consider uncertainties. By using importance analysis and minimal cut sets of the fault tree, the risk-based retrofitting options are determined. To show the applicability of the proposed methodology, it is applied on a benchmark reinforced concrete structure in Europe that was designed and built without observing the new seismic standards. The collapse fragility curve and annual risk of collapse of this structure are determined. Using minimal cut sets and importance analysis of the structure’s fault tree, two retrofitting options are identified. The first retrofitting option is decreased collapse risk by 43% and the second one decreased it by 60%.