This paper proposes a framework and its mathematical model for optimal routing and charging of an electric vehicle fleet for high-efficiency dynamic transit systems, while taking into account energy efficiency and charging price. Based on an extended pickup and delivery problem, an optimization model is formulated from the transit service providers’ perspective and is applied to an electric vehicle (EV) fleet with economically efficient but small batteries in very urbanized areas. It aims to determine the best route from the origin to the final destination for each EV to satisfy the welfare of all passengers (e.g., travel time and passengers’ travel distance), while maximizing the energy efficiency (e.g., by reducing fuel and charging cost), subject to local/global constraints (e.g., EV charging station availability and battery state-of-charge dynamics). This optimization model is solved as a mixed-integer quadratically constrained programming problem. This paper also explores the potential impact of EV fleet of dynamic commuter transit services on electric distribution systems, such as increased average load.