Abstract This article introduces an effective stochastic operation framework for optimal energy management of the shipboard power systems including large, nonlinear and dynamic loads. The proposed framework divides the ship power system into several agents, which coordinate with each other based on their demands/supplies until. The alternating direction method of multipliers (ADMM) is deployed as the multi-agent framework to solve the reformulated distributed energy management problem in the ship. Two types of turbo-generators are considered in the proposed system model, including single-shaft and twin-shaft models, to increase the part-load efficiency in certain times when facing variable speed operation. The proposed distributed framework is equipped with a recursive mechanism, which helps the ship system for running optimal load scheduling when facing insufficient power generation. In order to model the uncertainty effects associated with the forecast error in the interval-ahead load demand, a stochastic framework based on unscented transform is devised which can work in the nonlinear and correlated environments of shipboard power systems. Due to the nonlinear cost function in each agent, a powerful optimization algorithm based on modified θ-firefly algorithm (Mθ-FOA) is proposed. This is a phasor algorithm, which helps for escaping from premature convergence and getting trapped in local optima. The appropriate performance of the proposed stochastic model is examined on the real dataset of a ship power system. The simulation results show the high robustness, guarantied consensus, economic operation and feasible solution when power generation shortage based on load shedding in the system.