This paper presents a cost estimation model for long-term pavement warranties with multiple distress indicators. One application area for such warranties involves performance-based specifications (PBSs). In contrast to traditional approaches, PBS gives contractors the flexibility to select construction methods, materials, and even design. However, the contractors then must warrant the performance of their work for a specified period of time. Therefore, an accurate estimation of the risks associated with the warranty is a significant cost issue for any contractor to cover potential risks while still being competitive in bidding. Quantitative evaluation of the cost of risk incurred by the warranty has several difficulties. The deterioration of a highway project is a complex process, which is affected by pavement structure, material, traffic load, and weather conditions. Based on a probabilistic risk analysis of failures of performance indicators, the resulting model can estimate the warranty cost at a detailed level. The application of the model has been demonstrated via a numerical case study using long-term pavement performance data.