Disruptions to electric vehicle charging infrastructure can hinder consumers’ confidence and impact the performance of shared electric vehicle (SEV) systems. This study focuses on SEV systems’ vulnerability to emerging cyberattacks at the system level utilizing city-scale SEV trajectory data in Beijing, China. A data-driven simulation model is developed to account for realistic charging demand–supply interactions extracted from the data. The results show that among different types of disruptions, cybersecurity threats present unique challenges to SEV systems. Compared with attacking the most highly utilized charging stations, attacking popular ones on the city’s outskirts is more likely to significantly increase stress on the charging infrastructure and reduce the accessibility of SEVs. Meanwhile, the interactions between SEVs and infrastructure could either amplify the impacts by triggering cascading failures or relieve the adversarial effects. These findings provide insights into designing policies and solutions to enhance the resilience of SEV systems against cyberattacks.