Fast and accurate risk stratification is essential in the emergency department (ED) as it allows clinicians to identify chest pain patients who are at high risk of cardiac complications and require intensive monitoring and early intervention. In this paper, we present a novel intelligent scoring system using heart rate variability, 12-lead electrocardiogram (ECG), and vital signs where a hybrid sampling-based ensemble learning strategy is proposed to handle data imbalance. The experiments were conducted on a dataset consisting of 564 chest pain patients recruited at the ED of a tertiary hospital. The proposed ensemble-based scoring system was compared with established scoring methods such as the modified early warning score and the thrombolysis in myocardial infarction score, and showed its effectiveness in predicting acute cardiac complications within 72 h in terms of the receiver operation characteristic analysis.