Hydraulic systems have the characteristics of strong fault concealment, powerful nonlinear time-varying signals, and a complex vibration transmission mechanism; hence, diagnosis of these systems is a challenge. To provide accurate diagnosis results automatically, numerous studies have been carried out. Among them, signal-based methods are commonly used, which employ signal processing techniques based on the state signal used for extracting features, and further input the features into the classifier for fault recognition. However, their main deficiencies include the following: (1) The features are manually designed and thus may have a lack of objectivity. (2) For signal processing, feature extraction and pattern recognition are conducted using independent models, which cannot be jointly optimized globally. (3) The machine learning algorithms adopted by these methods have a shallow architecture, which limits their capacity to deeply mine the essential features of a fault. As a breakthrough in artificial intelligence, deep learning holds the potential to overcome such deficiencies. Based on deep learning, deep neural networks (DNNs) can automatically learn the complex nonlinear relations implied in a signal, can be globally optimized, and can obtain the high-level features of multi-dimensional data. In this paper, the main technology used in an intelligent fault diagnosis and the current research status of hydraulic system fault diagnosis are summarized and analyzed. The significant prospect of applying deep learning in the field of intelligent fault diagnosis is presented, and the main ideas, methods, and principles of several typical DNNs are described and summarized. The commonality between a fault diagnosis and other issues regarding typical pattern recognition are analyzed, and research ideas for applying DNNs for hydraulic fault diagnosis are proposed. Meanwhile, the research advantages and development trend of DNNs (both domestically and overseas) as applied to an intelligent fault diagnosis are reviewed. Furthermore, the fault characteristics of a complex hydraulic system are summarized and discussed, and the key problems and possible research ideas of applying DNNs to an intelligent hydraulic fault diagnosis are presented and comprehensively analyzed.