With the evolution of the shipping market, artificial intelligence research using ship data is being actively conducted. Smart ships and reducing ship greenhouse gas emissions are among the most actively researched topics in the maritime transport industry. Owing to the massive advances in information and communications technology, the internet of things, and big data technologies, smart ships have emerged as a very promising proposition. Numerous methodologies and network architectures can smoothly collect data from ships that are currently in operation, as is currently done in research on reducing ship fuel consumption by deep learning or conventional methods. Many extensive studies of stacked autoencoders have been carried out in the past few years. However, prior studies have not addressed the development of algorithms or deep learning-based models to classify the operating states of ships. In this paper, we propose for the first time a deep learning-based stacked autoencoder model that can classify the operating state of a ship broadly into the categories of At Sea, Stand By, and In Port, using actual ship power load data. In order to maximize the model’s performance, the stacked autoencoder architecture, number of hidden layers, and number of neurons contained in each layer were measured by performance metrics such as true positive rate, false positive rate, Matthews correlation coefficient, and accuracy. It was found that the model’s performance was not always improved by increasing its complexity, so the feasibility of developing and utilizing an efficient model was verified by comparing it to real data. The best-performing model had a (5–128) structure with latent layer size 9. It achieved a true positive rate of 0.9035, a false positive rate of 0.0541, a Matthews correlation coefficient of 0.9054, and an accuracy of 0.9612, clearly demonstrating that deep learning can be used to analyze ship operating modes.