Deep pressure input is used to normalize physiological arousal due to stress. Wisdom tooth surgery is an invasive dental procedure with high stress levels, and an alleviation strategy is rarely applied during extraction. In this study, we investigated the effects of deep pressure input on autonomic responses to wisdom tooth extraction in healthy adults. Methods: A randomized, controlled, crossover design was used for dental patients who were allocated to experimental and control groups that received treatment with or without deep pressure input, respectively. Autonomic indicators, namely the heart rate (HR), percentage of low-frequency (LF) HR variability (LF-HRV), percentage of high-frequency (HF) HRV (HF-HRV), and LF/HF HRV ratio (LF/HF-HRV), were assessed at the baseline, during wisdom tooth extraction, and in the posttreatment phase. Results: Wisdom tooth extraction caused significant autonomic parameter changes in both groups; however, differential response patterns were observed between the two groups. In particular, deep pressure input in the experimental group was associated with higher HF-HRV and lower LF/HF-HRV during extraction compared with those in the control group. Conclusion: LF/HF-HRV measurement revealed balanced sympathovagal activation in response to deep pressure application. The results suggest that the application of deep pressure alters the response of HF-HRV and facilitates maintaining sympathovagal balance during wisdom tooth extraction.