Dating back to the 19th century, the discovery of processing stages has been of great interest to researchers in cognitive science. The goal of this paper is to demonstrate the validity of a recently developed method, hidden semi-Markov model multivariate pattern analysis (HsMM-MVPA), for discovering stages directly from EEG data, in contrast to classical reaction-time-based methods. To test the validity of stages discovered with the HsMM-MVPA method, we applied it to two relatively simple tasks where the interpretation of processing stages is straightforward. In these visual discrimination EEG data experiments, perceptual processing and decision difficulty were manipulated. The HsMM-MVPA revealed that participants progressed through five cognitive processing stages while performing these tasks. The brain activation of one of those stages was dependent on perceptual processing, whereas the brain activation and the duration of two other stages were dependent on decision difficulty. In addition, evidence accumulation models (EAMs) were used to assess to what extent the results of HsMM-MVPA are comparable to standard reaction-time-based methods. Consistent with the HsMM-MVPA results, EAMs showed that nondecision time varied with perceptual difficulty and drift rate varied with decision difficulty. Moreover, nondecision and decision time of the EAMs correlated highly with the first two and last three stages of the HsMM-MVPA, respectively, indicating that the HsMM-MVPA gives a more detailed description of stages discovered with this more classical method. The results demonstrate that cognitive stages can be robustly inferred with the HsMM-MVPA.