To ensure safe runway operations and make the best use of maintenance funds, cracks in runway pavements should be repaired according to severity and maintenance needs. In traditional pavement maintenance management, priority of crack repair is determined by crack width, length, density, extent, and sometimes location. However, this basis for prioritization is not entirely satisfactory because it does not consider aircraft operational characteristics and may not assign priority correctly. One possible improvement is to apply the concept of failure risk in analyzing runway pavement cracks and to assign higher priority to cracks with higher risk of failure or interference with safe aircraft operations. This paper illustrates how this concept can be incorporated into maintenance management of cracks in runway pavements by employing structural analysis that uses a mechanistic approach. In addition to the dimensions and characteristics of cracks mentioned earlier, crack depth, aircraft loading, and operational characteristics have to be considered. In the analysis of failure risk, the proposed methodology considers frequency of different aircraft types and statistical distributions of their wheel loadings during landings and takeoffs, touchdown points, and lateral wanders. For each crack with known dimensions and location, the stresses and strains under load are computed by using finite element analysis. The crack’s failure risk is expressed by means of Miner’s rule, which in turn forms the basis for maintenance prioritization. The detailed steps of the proposed methodology are described in this paper, and a numerical example is presented to demonstrate the application of the methodology.