Different methods and procedures have been developed to define prioritisation strategies of retrofit interventions aimed at reducing the seismic risk of school buildings on a large territorial scale. However, these approaches fail to demonstrate how risk analysis has been used successfully to quantitatively assess and select the optimal risk management decision. This article proposes innovative and useful metrics to measure the potential costs and benefits related to the prioritisation of retrofit intervention and the resilience of the analysed school system by directly integrating engineering, organisational, socio-economic and political aspects in the realm of seismic resilience assessment. Based on probabilistic risk assessments considering the new vulnerability of the prioritised school buildings, these measures could predict the expected economic and functional losses associated with a disastrous seismic event, as well as the possible post-disaster recovery of the system. In order to help decision-makers in selecting the optimal mitigation strategy with a multidisciplinary and multidimensional perspective, different political scenarios, the relative prioritisations of interventions and their intervention options are also defined. The proposed framework is demonstrated in a complex case study of 1,825 public schools in the Lima metropolitan area, Peru. Policymakers, planners and engineering professionals could benefit from results.