Modern vehicles are increasingly getting connected within the vehicles, with other systems, leading to more concerns about security. Controller area network (CAN) has become a de-facto standard for connecting internal vehicles’ components. However, it lacks security features. Conventional security mechanisms fail to protect in-vehicle networks from attacks, requiring the development of an effective intrusion detection system (IDS). This work develops an IDS for in-vehicle networks called IDS-IVN based on a compact representation of location invariant and time-variant traffic features using deep learning. The IDS-IVN uses convolutional neural and long–short-term memory networks as encoder/decoder functions of autoencoder networks to extract features from raw data and classify them using latent space representation into intrusive and non-intrusive classes. A benchmark real-time ROAD dataset is used to demonstrate the IDS-IVN’s performance compared to the existing methods. IDS-IVN reports 99% accuracy with a 0.32% low false-positive rate for detecting intrusions.