Typical electric vehicles (EVs) should be recharged multiple times to reach a long distance due to the limited travel ranges. The EV flow covering problem determines the locations of charging stations to maximize the “covered” OD flows, respecting a given budget for the new charging stations. This paper proposes an exact algorithm for solving the problem by considering the heterogeneous EV chargers, nonlinear charging time, and route deviations from the shortest distance paths. We develop an exact Benders decomposition-based algorithm, in which the Benders subproblem utilizes a nested cut-generation via a customized labeling algorithm. Two methods for solving the Benders subproblem are developed, which are combined to accelerate the Benders cut generation. In addition, we present a heuristic algorithm based on the proposed exact algorithm for the larger-sized problems. The computational results show that the proposed algorithm could solve real-life problems. Especially, the heuristic algorithm could solve problems up to 339 nodes and 500 km of the EV’s travel range. The extensive computational study shows that addressing the multiple charger types, the charging time, and the deviation routes can be crucial to provide realistic charging infrastructure for EVs.