Objectives: To investigate the correlation of anxiety or depression mood with physical stress of 59 participants (29 who complained of chronic headache and 30 who did not complain of headache) using a questionnaire on chronic headache symptoms, Beck Anxiety Inventory (BAI), Beck Depression Inventory (BDI), and Heart Rate Variability (HRV). Methods: In this study, medical records of 59 participants (29 who complained of chronic headache and 30 who did not complain of headache) who completed the BAI, BDI, HRV, and Questionnaire for chronic headache symptoms were evaluated. All data were analyzed using SPSS (Statistical Package for the Social Sciences, Version 26.0). Descriptive Analysis, Mann-Whitney U test, Chi square test (Fisher’s exact test), and Pearson correlation coefficient were used for data analysis. Results: 1. The chronic headache group had significantly lower SDNN, RMSSD, TP, LF, and HF values on HRV than the general control group. 2. As BAI and BDI scores of the chronic headache group increased, the overall HRV value tended to decrease, indicating a deep association. 3. There was a negative association between BDI and HRV values in the chronic headache group, although such association was not statistically significant. Conclusions: BDI can be negatively correlated with HRV (SDNN, RMSSD, TP, LF, HF) in chronic headache patients.