This research was conducted to propose the design methodologies of post-tensioned concrete pavements (PTCPs) for specialized section pavements. The specialized sections considered in this study included bus stop sections in urban bus-only lanes and culvert existing highway sections that often showed severe failures. The PTCP designs of those specialized sections were performed based on both the stresses and the fatigue failures, and more conservative design results were selected. In the stress based design, the maximum tensile stress under extreme load conditions was obtained using finite element analyses first. Then, the number of tendons and the tendon spacing were determined so that the tensile stress was less than the allowable flexural strength. The AASHTO fatigue failure equations were used in the fatigue failure based design. From this study, the design methodologies of PTCP for bus stop sections in bus-only lanes and culvert existing highway sections were successfully suggested.