Airports play a critical role in transporting goods and passengers and supporting the growth of the world economy. Airports spend huge sums annually to maintain and improve pavement functions by expanding the runways, taxiways, and aprons, and perform routine maintenance and rehabilitation of the existing pavements. Besides the traditional direct costs, a comprehensive airport pavement management system should also consider indirect costs such as fuel, crew, passenger delay, aircraft maintenance, and loss of airport revenue when conducting a life-cycle cost analysis (LCCA). Engineers, managers, and stakeholders can make better decisions on the appropriate pavement maintenance and rehabilitation strategies by performing economic analyses of the direct and indirect costs. This study performed probabilistic and deterministic LCCA to contrast the effect of direct costs vis-a-vis indirect costs in airport pavement management. A case study found that indirect costs could contribute up to 20% of the total costs when using Portland cement concrete (PCC), hot mixed asphalt (HMA), and crack seat overlay (CSOL). Previous research did not give much attention to maintenance since the researchers believed that routine maintenance makes up only an insignificant percentage of the LCCA. However, routine maintenance of HMA and CSOL makes up 10.2% and 14.2% of the total cost. The rehabilitation cost of PCC makes up 16.3% of the total cost, and the rehabilitation cost for HMA and CSOL makes up 25.4% and 35.2% of the total cost.