Rapid development of electric vehicles holds the promise to significantly mitigate greenhouse gas emissions. However, the lack of pervasive en-route charging infrastructure on regional highway networks hinders the use of electric vehicles for long-distance intercity trips. Traditionally, transportation and power systems are often studied separately, each by itself as a complex system. This paper proposes a system of systems modeling framework for planning charging infrastructure deployment in intercity transportation networks while considering users’ travel behavior and coupling relationships between transportation and power systems. The aim is at facilitating long-distance electric vehicle travels and providing an effective and comprehensive tool to evaluate the total emissions from both the transportation and power sectors. We look at a somewhat “forward-looking” problem in which the charging loads of widely-adopted electric vehicles induce interdependence between the power and the transportation sectors. A general equilibrium modeling framework is developed to capture the interdependencies among charging infrastructure design, users’ travel behaviors, and power sector operations. An iterative solution approach is proposed to solve the overall equilibrium between the transportation and power sectors, and a heuristic algorithm is developed to solve the bi-level subproblem for the charging infrastructure deployment. Numerical experiments based on a semi-realistic case study are performed to demonstrate the applicability of the proposed modeling and solution approach.