Predictive analytics is an increasingly popular tool for enhancing decision-making processes but is in many business settings based on rule-based models. These rule-based models reach their limits in complex settings. This study compares the performance of a rule-based system with a customised LSTM encoder-decoder deep learning model for predicting train delays. For this, we use a purposefully built real-world dataset on railway transportation, where trains’ interdependence over the network makes delay prediction more difficult. Results show that the deep learning model, which incorporates rich spatiotemporal interdependency information in real-time, outperforms the rule-based system by 18%, with the difference increasing to above 23% with higher complexity. The study also dissects the performance difference across different settings: dense versus rural areas, peak versus off-peak hours, low versus high delay, and before versus during the COVID-19 pandemic. The deep learning model is implemented as a proof of concept for decision support within Belgium’s railway infrastructure company Infrabel.