Colombian seismic code NSR-98 establishes the requirement for the seismic vulnerability analysis and, if necessary, the strengthening of public facilities (schools). Due to the investments required by risk reduction programs, it is necessary to establish criteria for assigning priorities for the interventions. This article proposes a methodology for obtaining a Benefit-Cost Ratio (BCR) at the subnational level, by assessing the expected annual average loss of the built area of public schools and the retrofitting cost. The BCR is estimated as the difference between the estimates of the net present value for status quo and retrofitted states, these two divided by the retrofitting costs. According to the BCR, 47.3% of the total school built area of Colombia should be retrofitted where the retrofitting costs correspond to 25% of the total investment. Proposed BCR is useful for prioritizing regions in function of the feasibility of reducing the seismic vulnerability of the schools.