This paper introduces an optimal energy control method whose rule-based control employs the equivalent consumption minimization strategy as the design standard to support a neural network technique. Using the proposed control method, the output command values for each power source based on the load of the ship and the state of charge of the battery satisfy the target of energy optimization. Based on the rules, the load of the ship and the state of charge of the battery were the input in the neural network, and the outputs of two generators were recorded as the output values of the neural network. To optimize the weights of the neural network and reduce the error between the predicted values and results, the Bayesian regularization method was employed, and a single hidden layer with 20 nodes, 2 input layers, and 2 output layers were considered. For the hidden layer, the tansigmoid function was applied, and for the activation functions of the output layers, linear functions were adopted considering the correlation between the input and output data used for training the neural network. The propulsion motor was fitted with a speed controller to ensure a stable speed, and a torque load was applied on the propulsion motor. To verify the accuracy of the neural network learning, a generator–battery hybrid system simulation was conducted using MATLAB Simulink, and the neural network learned values were compared with the generator output command values obtained based on the load of the ship and the battery state of charge. Additionally, it was confirmed that the generator command values were consistent with the neural network learned values, and the stability of the system was maintained by controlling the speed, voltage, and current control of the propulsion motor under various loads of the ship and different battery charge statuses.