Variations in the autonomic nervous system activity during exercise therapy in patients with cardiovascular diseases may lead to adverse events. Aromatherapy may reduce these adverse events by enhancing parasympathetic nervous activity (PNA). However, the effects of aromatherapy during exercise remain relatively unknown. This study aimed to evaluate the effect of aromatherapy on autonomic nervous activity during exercise and recovery. This randomized crossover study included 20 healthy men subjected to both aroma and placebo conditions which involved rest and moderate-intensity aerobic exercise on a cycle ergometer, followed by recovery. Blood pressure, heart rate variability indices, and SpO2 were measured during the rest, exercise, and recovery phases. Moreover, aroma preferences and emotional changes in response to the aroma were assessed. Under the placebo condition, high frequency (HF), root mean square of successive differences indices, and heart rate showed delayed recovery (P < 0.05). Furthermore, a moderate positive correlation was identified between aroma preference, pleasant emotions induced by aromatherapy, and the HF index (P < 0.05). These results indicate that aromatherapy facilitates the recovery of PNA after exercise. Furthermore, these effects were more pronounced among individuals who exhibited a stronger preference for and more positive emotions toward aromas.