Point clouds consist of 3D data points and are among the most considerable data formats for 3D representations. Their popularity is due to their broad application areas, such as robotics and autonomous driving, and their employment in basic 3D vision tasks such as segmentation, classification, and detection. However, processing point clouds is challenging compared to other visual forms such as images, mainly due to their unstructured nature. Deep learning (DL) has been established as a powerful tool for data processing, reporting remarkable performance enhancements compared to traditional methods for all basic 2D vision tasks. However new challenges are emerging when it comes to processing unstructured 3D point clouds. This work aims to guide future research by providing a systematic review of DL on 3D point clouds, holistically covering all 3D vision tasks. 3D technologies of point cloud formation are reviewed and compared to each other. The application of DL methods for point cloud processing is discussed, and state-of-the-art models’ performances are compared focusing on challenges and solutions. Moreover, in this work the most popular 3D point cloud benchmark datasets are summarized based on their task-oriented applications, aiming to highlight existing constraints and to comparatively evaluate them. Future research directions and upcoming trends are also highlighted.