Anxiety is one of the most frequently diagnosed emotional disorders after a mild traumatic brain injury (mTBI); however, predictors of anxiety after an mTBI remain uncertain. Recent research indicated that anxiety is associated with abnormalities in the autonomic nervous system (ANS) which can be evaluated by a power spectral analysis of heart rate variability (HRV). In this study, we investigated whether a frequency-domain analysis of HRV could correlate with the occurrence of anxiety in mTBI patients. We recruited 165 Taiwanese patients diagnosed with an mTBI and 82 volunteer healthy controls from three affiliated hospitals of Taipei Medical University during 2010-2014. The Beck Anxiety Inventory (BAI) was assessed at the 1st, 6th, and 12th weeks. We found that mTBI patients were more vulnerable to anxiety compared to healthy controls. The power spectral density of HRV was significantly lower in mTBI patients than in healthy controls. A correlation analysis indicated that anxiety was negatively significantly correlated with low- and high-frequency power at the 6th week. Our study suggests the clinical usefulness of HRV as a potential noninvasive tool for evaluating later anxiety in mTBI patients.