The growing energy demand and population raising require alternative, clean, and sustainable energy systems. During the last few years, hydrogen energy has proven to be a crucial factor under the current conditions. Although the energy conversion process in polymer electrolyte fuel cells (PEFCs) is clean and noiseless since the only by-products are heat and water, the inside phenomena are not simple. As a result, correct monitoring of the health situation of the device is required to perform efficiently. This paper aims to explore and evaluate the machine learning (ML) and deep learning (DL) models for predicting classification fault detection in PEFCs. It represents a support for decision-making by the fuel cell operator or user. Seven ML and DL model classifiers are considered. A database comprising 182,156 records and 20 variables arising from the fuel cell's energy conversion process and operating conditions is considered. This dataset is unbalanced; therefore, techniques to balance are applied and analyzed in the training and testing of several models. The results showed that the logistic regression (LR), k-nearest neighbor (KNN), decision tree (DT), random forest (RF), and Naive Bayes (NB) models present similar and optimal trends in terms of performance indicators and computational cost; unlike support vector machine (SMV) and multi-layer perceptron (MLP) whose performance is affected when the data is balanced and even presents a higher computational cost. Therefore, it is a novel approach for fault detection analysis in PEFC that combines the interpretability of different ML and DL algorithms while addressing data imbalance, so common in the real world, using resampling techniques. This methodology provides clear information for the model decision-making process, improving confidence and facilitating further optimization; in contrast to traditional physics-based models, paving the way for data-driven control strategies.