We investigated the muscle fatigue and degree of discomfort for seven combinations of positions in a touchpad and two click‐buttons (one hand: center, midright, and right in position of touchpad and buttons; two hands: all centered, centered touchpad and left buttons, right touchpad and centered buttons, and right touchpad and left buttons) while using a laptop PC. Sixteen subjects participated in tasks involving the operation of a touchpad and two click‐buttons. The muscle fatigue was evaluated by applying median frequency electromyography (EMG) for 5 minutes to the subjects while they were performing each task, and the overall degree of discomfort was measured by fuzzy logic questions after the completion of each condition. When using only one hand, the right position resulted in the lowest muscle fatigue and degree of discomfort in comparison with the other conditions (p < .05). When using two hands, the right placement of the touchpad and the left one of the buttons showed the lowest results in both the muscle fatigue and degree of discomfort (p < .05). On the other hand, the traditional centered locations in the case of both one hand and two hands were the most disadvantageous for the shoulder and wrist. The results indicate that the traditional location of the touchpad and click‐buttons in the center induced abduction in both the shoulder and the wrist, which was expressed as an increase in muscle fatigue and overall discomfort. Therefore, developing a configuration in which it is possible to adjust the positions of the touchpad and buttons based on the user's preference is required.