We investigated the effects of two prominent aromas, lavender and jasmine, on peripheral and cardiac autonomic nervous system activity under stressful conditions, in a highly reproducible manner using an olfactometer. The subjects comprised 17 healthy men aged 20–24 years. In this within-subjects study design, all subjects were required to perform a simple calculation task for 30 min to induce cognitive stress, and aroma from lavender or jasmine essential oil or a control stimulus was inhaled intermittently (first 20 s of each 1-min interval) to prevent olfactory fatigue. The control stimulus was provided by triethyl citrate, an odourless solvent. In addition to subjective psychological assessments using a visual analogue scale, the temperature at the tip of the nose and cardiac activity on electrocardiogram were recorded as indices of peripheral and cardiac autonomic nervous system activities, respectively. Significant decreases in nose tip temperature and high-frequency (HF) component of heart rate variability (HRV), and a significant increase in heart rate were observed under all three conditions. However, compared with the control condition, lavender inhalation induced significantly greater decreases in nose tip temperature (p < 0.01) and HF component of HRV (p < 0.01), which indicated greater enhancement of sympathetic nervous system activity and suppression of parasympathetic nervous system activity. On the other hand, lavender inhalation induced a positive mood, less subjective stress, and increased concentration during the task (p < 0.01). These contradictory results of enhanced physiological stress response and lower subjective stress induced by lavender inhalation under stressful conditions suggest that lavender aroma may have effects other than sedation. Further studies are necessary to further clarify these effects.