This study analyzed variations of learning stress by comparing the salivary cortisol levels of students who participated in Earth Science inquiry activities. The cortisol concentrations between the pre- and post-inquiries of the sample of 34 university students, who had taken the course of ‘Basic Earth Science and Experiments’, were analyzed. The Earth Science inquiries consisted of geology and astronomy activities. The observational geology activities consisted of a session of ‘structure contours and map patterns’ and the cognitive astronomy activities consisted of a session of ‘representations of horizontal and equatorial coordinates’. These Earth Science inquiry activities were found to cause students to have anxiety, and the thought processes that these activities involved were found to cause learning stress. The variations in cortisol concentrations of students increased by 1.6±5.9 ng mL−1 after conducting observational activities in geology compared with 2.1±6.2 ng mL−1 after doing cognitive activities in astronomy. The analysis of the observational activities in the geology inquiry activities indicated that they were consistent with low levels of learning stress. Conversely, the analysis of the cognitive activities in the astronomy inquiry activities showed significant individual variations in cortisol concentrations. Furthermore, individual differences in cognitive ability were reflected in the astronomy inquiry activities. While students, who received high scores, exhibited low levels of stress in the geology inquiry activities, they showed high levels of stress in the astronomy inquiry activities. It was concluded that, in the case of students with high scores in the study, the level of learning stress increased due to the raised anxiety in cognitive inquiry activities. In contrast, students, who received low scores in the study, exhibited high levels of stress in the geology inquiry activities, and low levels of stress in the astronomy inquiry activities.