The growth of information technologies has driven the development of the transportation sector, including connected and autonomous vehicles. Due to its communication capabilities, the controller area network (CAN) is the most widely used in-vehicle communication protocol. However, CAN lacks suitable security mechanisms such as message authentication and encryption. This makes the CAN bus vulnerable to numerous cyberattacks. Not only are these attacks a threat the information security and privacy, but they can also directly affect the safety of drivers, passengers and the surrounding environment of the moving vehicles. This paper presents CAN-CID, a context-aware intrusion detection system (IDS) to detect cyberattacks on the CAN bus, which would be suitable for deployment in automobiles including military vehicles, passenger cars, commercial vehicles and other CAN-based applications such as aerospace, industrial automation and medical equipment. CAN-CID is an ensemble model of a gated recurrent unit (GRU) network and a time-based model. A GRU algorithm works by learning to predict the centre ID of a CAN ID sequence, and ID-based probabilistic thresholds are used to identify anomalous IDs, whereas the time-based model identifies anomalous IDs using time-based thresholds. The number of anomalies compared to the total number of IDs over an observation window is used to classify the window status as anomalous or benign. The proposed model uses only benign data for training and threshold estimation, avoiding the need to collect realistic attack data to train the algorithm. The performance of the CAN-CID model was tested against three datasets over a range of 16 attacks, including fabrication and more sophisticated masquerade attacks. The CAN-CID model achieved an F1-Score of over 99% for 13 of those attacks and outperformed benchmark models from the literature for all attacks, with near real-time detection latency.