One of the most demanded competencies of an oral health professional such as an oral pathologist is the ability to make clinical decisions. The purpose of this study was to examine the neurological differences between beginners and experts in the clinical decision-making process which consisting of complex, dynamic and sophisticated cognitive processes, and to identify the characteristics of experts based on the brain by comparing EEG activity. This study conducted experimental design with 10 dentists with more than 10 years of clinical experience and 10 students with short clinical experience as beginners as a fourth year student before graduation. The hypothesis-oriented algorithm proposed in HOAC II was used. As a standard, the clinical decision-making stage of the dentist was divided into three stages, and an event was developed and an experiment was designed for measuring EEG for each stage. The cerebral activity distribution patterns of the two groups were measured with EEG, compared and analyzed with pre-processing process using EEGlab. As a result, the difference in the auditory information was not noticeable between the novice and the expert, but the difference between the group of the novice and the expert appeared in the visual data and the radiographic data. In the case of beginners, the activity was higher in the left hemisphere, and in the case of experts, both brains were activated. The results of this study are intended to present objective information based on brain-based analysis of differences that appear in the clinical decision-making process of experts and beginners. It can be used as basic research data to present the brain-based characteristic analysis of dentist experts.