Presently, Supervisory Control and Data Acquisition (SCADA) systems are broadly adopted in remote monitoring large-scale production systems and modern power grids. However, SCADA systems are continuously exposed to various heterogeneous cyberattacks, making the detection task using the conventional intrusion detection systems (IDSs) very challenging. Furthermore, conventional security solutions, such as firewalls, and antivirus software, are not appropriate for fully protecting SCADA systems because they have distinct specifications. Thus, accurately detecting cyber-attacks in critical SCADA systems is undoubtedly indispensable to enhance their resilience, ensure safe operations, and avoid costly maintenance. The overarching goal of this paper is to detect malicious intrusions that already detoured traditional IDS and firewalls. In this paper, a stacked deep learning method is introduced to identify malicious attacks targeting SCADA systems. Specifically, we investigate the feasibility of a deep learning approach for intrusion detection in SCADA systems. Real data sets from two laboratory-scale SCADA systems, a two-line three-bus power transmission system and a gas pipeline are used to evaluate the proposed method’s performance. The results of this investigation show the satisfying detection performance of the proposed stacked deep learning approach. This study also showed that the proposed approach outperformed the standalone deep learning models and the state-of-the-art algorithms, including Nearest neighbor, Random forests, Naive Bayes, Adaboost, Support Vector Machine, and oneR. Besides detecting the malicious attacks, we also investigate the feature importance of the cyber-attacks detection process using the Random Forest procedure, which helps design more parsimonious models.