Electric transport systems and renewable energy sources (RESs) have recently attracted significant interest, because of the limitations and drawbacks of fossil fuels and the growing demand for utilization of clean energy. Suitable paradigms are needed to manage the atypical and heterogeneous load of electric vehicles (EVs), the intermittent nature of RESs, and the changeability of electrical loads in power networks. The technical and commercial operation of an integrated system comprising an electric transportation system with a battery-powered bus [electric bus (eBus)] charging station and an EV parking lot, integrated with solar photovoltaic (PV) generation, and combined with a battery storage system (BSS), as a virtual energy hub (VEH) is proposed. Moreover, a cooperative decision-making (CDM) strategy is proposed for the VEH, where the active and reactive power flows and the economic operation of the VEH are scheduled using a novel three-stage cooperative control system. A supervisory control system is developed using agents to realize the scheduled CDM of the VEH and to assign the control parameters for the provision of ancillary services. The VEH agent can operate autonomously during the real-time operation to cope with the volatility of the power system based on the optimal predetermined set points from the grid agent. The effectiveness of the CDM methodology is studied and evaluated through different realistic scenarios. The results show that the proposed CDM can organize the effective energy management (EM) with a minimum operational cost to the VEH. Furthermore, because of the designed supervisory control and the provision of ancillary services using the VEH, the grid requirements can be effectively managed.