In a usual seismic damage estimation by a local government, relations between its damage estimation and a local disaster prevention plan or earthquake disaster prevention are not always clear, and it often depends on precedent examples or individual previous experience and intuition of a person-in-charge to select countermeasures in such a plan or policies. From a view point of the so-called accountability of a local government, we need to establish a practical and rational decision making method for earthquake disaster prevention planning. Here we take Fukuoka City, one of twelve designated big cities in Japan, as a target of our case study. First we estimate the building damage from a hypothesized earthquake on the Kego fault, which is running across Fukuoka City. Then we consider various investment plans against the estimated building damage. Finally, we perform the cost-effectiveness analysis for these plans and show how to choose a most efficient plan from an economical point of view. As a result, we found that we can decide priority of different plans in a united manner based on the aseismic safety improvement per unit cost for each plan.