The purpose of this study was to evaluate muscle activation and fatigue in the operator during tooth preparation and intraoral scanning by simulating these tasks in two types of dental unit chair systems (UCS). Six participants were recruited, and the above tasks were simulated. Electrodes were placed on the skin over five types of muscles (arm, neck, and shoulder muscles), and the maximal voluntary contraction (MVC) was measured. Electromyography (EMG) was assessed during the simulation, and EMG values were normalized using MVC. The root mean square (RMS) EMG (%MVC) and muscle fatigue (%) were calculated. Owing to a lack of normal distribution of the data, Mann–Whitney U test and Kruskal–Wallis H test were performed for statistical comparison, and Bonferroni adjustment was performed for multiple comparisons (α = 0.05). There was no significant difference in RMS EMG between the two types of dental UCS (intraoral scanning, p = 0.237; tooth preparation, p = 0.543). Moreover, the RMS EMG and muscle fatigue were not significantly different between the two tasks (p > 0.05). There was significant muscle fatigue after the intraoral scanner use was simulated thrice (p < 0.001). It is necessary to refrain from performing continuous intraoral scanning and tooth preparation and to take appropriate rest to reduce the incidence of musculoskeletal disorders in dentists in clinical settings.