Cortisol secretion after awakening, an index of hypothalamus–pituitary–adrenal axis activity, appears to be related to psychosocial stressors, or to symptoms caused by psychosocial stressors. The relationship between the quality, duration, and magnitude of psychosocial factors and cortisol secretion is however, unclear. Therefore, the effect of episodic stress associated with writing a graduation thesis on cortisol secretion after awakening was investigated. Saliva samples were collected from 10 undergraduate students at awakening, and 30, 45, and 60 min after awakening 1 month, 2 weeks, and a few days before the thesis submission and 1 week after the submission. They also completed the Short form of Profile of Moods Scale (POMS-S) on the night before each sampling. Results indicated that cortisol levels were higher a few days before the thesis submission compared to 1 month before submission. Scores of “Fatigue” and “Tension-Anxiety” in POMS-S were also higher a few days before submission. These results suggest that episodic stress associated with writing a graduation thesis caused an increase in cortisol levels after awakening.