Deep neural networks (DNNs) have achieved tremendous success in making accurate predictions for computer vision, natural language processing, as well as science and engineering domains. However, it is also well-recognized that DNNs sometimes make unexpected, incorrect, but overconfident predictions. This can cause serious consequences in high-stake applications, such as autonomous driving, medical diagnosis, and disaster response. Uncertainty quantification (UQ) aims to estimate the confidence of DNN predictions beyond prediction accuracy. In recent years, many UQ methods have been developed for DNNs. It is of great practical value to systematically categorize these UQ methods and compare their advantages and disadvantages. However, existing surveys mostly focus on categorizing UQ methodologies from a neural network architecture perspective or a Bayesian perspective and ignore the source of uncertainty that each methodology can incorporate, making it difficult to select an appropriate UQ method in practice. To fill the gap, this paper presents a systematic taxonomy of UQ methods for DNNs based on the types of uncertainty sources (data uncertainty versus model uncertainty). We summarize the advantages and disadvantages of methods in each category. We show how our taxonomy of UQ methodologies can potentially help guide the choice of UQ method in different machine learning problems (e.g., active learning, robustness, and reinforcement learning). We also identify current research gaps and propose several future research directions.