Background: the Skill, Rule, and Knowledge (S-R-K) model is a framework used to describe and analyze human behaviour and decision-making in complex environments based on the nature of the task and kind of cognitive control required. The S-R-K model is particularly useful in fields like human factor engineering, system design, and safety-critical industries because it helps to understand human errors and how they relate to different levels of cognitive control. However, the S-R-K model is still qualitative and lacks specific and quantifiable metrics for determining what kind of cognitive control a person is using at any given time. This aspect makes difficult to directly measure and compare performance across the three levels. This study aimed therefore to characterize the S-R-K model from a neurophysiological perspective by analyzing the operator’s cerebral cortical activity. Methods: in this study, participants carried out experimental tasks able to replicate the Skill (tracking task), Rule (rule-based navigation) and Knowledge conditions (unfamiliar situations). Results: participants’ Electroencephalogram (EEG) was recorded during tasks execution and then Global Field Power (GFP) was estimated in the different EEG frequency bands. Brodmann areas (BAs) and EEG features were then used to characterize the S-R-K pattern over the cerebral cortex and as inputs to build up the machine learning-based model to estimate participants’ cognitive control behaviours while dealing with tasks. Conclusions: the results demonstrate the possibility of objectively measuring the different S, R and K levels in terms of brain activations. Furthermore, such evidence is consistent with the scientific literature in terms of cognitive functions corresponding to the different levels of cognitive control.