Intrusion detection systems (IDSs) are intrinsically linked to a comprehensive solution of cyberattacks prevention instruments. To achieve a higher detection rate, the ability to design an improved detection framework is sought after, particularly when utilizing ensemble learners. Designing an ensemble often lies in two main challenges such as the choice of available base classifiers and combiner methods. This paper performs an overview of how ensemble learners are exploited in IDSs by means of systematic mapping study. We collected and analyzed 124 prominent publications from the existing literature. The selected publications were then mapped into several categories such as years of publications, publication venues, datasets used, ensemble methods, and IDS techniques. Furthermore, this study reports and analyzes an empirical investigation of a new classifier ensemble approach, called stack of ensemble (SoE) for anomaly-based IDS. The SoE is an ensemble classifier that adopts parallel architecture to combine three individual ensemble learners such as random forest, gradient boosting machine, and extreme gradient boosting machine in a homogeneous manner. The performance significance among classification algorithms is statistically examined in terms of their Matthews correlation coefficients, accuracies, false positive rates, and area under ROC curve metrics. Our study fills the gap in current literature concerning an up-to-date systematic mapping study, not to mention an extensive empirical evaluation of the recent advances of ensemble learning techniques applied to IDSs.