In transboundary areas, harmonizing risk assessment across borders is essential for effective risk management. However, differing methodologies for seismic risk assessment used by different countries can yield unequal results on either side of the border. This study presents a framework for harmonized cross-border time-based risk assessment, built upon established seismic risk assessment practices at the national level. The framework considers cross-border hazard, exposure, fragility, and consequence models, aiming to harmonize different data sources, methodologies, and models. An emphasis is given to a heuristic approach for the harmonization of fragility curves defined in the national fragility models. The proposed framework is implemented for the Italian-Slovenian cross-border region defined by municipalities near Gorizia and Nova Gorica. The results reveal differences in seismic risk levels between the building stocks on the Slovenian and Italian sides, primarily due to higher building density, seismic hazard, and vulnerability in Italy, while the seismic risk to people was observed to be nearly equal for urban centres like Gorizia and Nova Gorica. These findings can be used to design joint strategies for long-term risk management of the analysed cross-border region. However, further research is needed, particularly to overcome limitations related to the data sources of the exposure models and methodologies for fragility and consequence models, which can be addressed over a long period through systematic standardization of cross-border seismic risk assessment.