In the 2000s, the liberalization of the rail markets for freight and passenger travel opened up the competition. Nowadays, local, regional, and long-distance passenger rail are gradually following suit. As a consequence of the paradigm of realizing smart and sustainable cities, the operators of local railway infrastructures (i.e., metro, light railway, and commuter) are studying strategies to improve the energy efficiency of the overall system. The operators are thus involved in renewing technological infrastructures and examining new operation models for coordinating the motion of the trains fleet. With this regard, the present work proposes a timetable adjustment approach to reduce energy consumption in metro rail transit systems. In addition, a centralized control strategy to manage the output voltage of Traction Power Substations (TPSs), train regenerative power, and charge/discharge power profiles of off-board Energy Storage Systems (ESSs) is proposed. The approach is based on a two-step procedure aimed at optimally allocating the layover time among the train stops. This approach is formulated as an optimization problem, which consider the adopted control strategy, because of the correlation between control actions and timetable. Numerical examples have been carried out based on the real data from metro line 1 of Naples, (Italy). The results highlight the capability of the strategy to achieve relevant results in terms of energy saving. In addition, the advantages introduced by the proposed centralized control strategy are emphasized through a comparison with the conventional local control strategy.