<i>Background:</i> Functional somatic symptoms (FSS) are symptoms not explained by underlying organic pathology. It has frequently been suggested that dysfunction of the autonomic nervous system (ANS) contributes to the development of FSS. We hypothesized that decreased cardiac vagal activity is cross-sectionally and prospectively associated with the number of FSS in the general population. <i>Methods:</i> This study was performed in a population-based cohort of 774 adults (45.1% male, mean age ± SD 53.5 ± 10.7 years). Participants completed the somatization section of the Composite International Diagnostic Interview surveying the presence of 43 FSS. ANS function was assessed by spectral analysis of heart rate variability in the high-frequency band (HRV-HF), reflecting cardiac vagal activity. Follow-up measurements of HRV-HF and FSS were performed approximately 2 years later. <i>Results:</i> Linear regression analyses, with adjustments for gender, age, body mass index, anxiety, depression, smoking, alcohol use, and frequency of exercise, revealed an interaction of cardiac vagal activity with age: HRV-HF was negatively associated with FSS in adults ≤52 years of age (β = –0.12, t = –2.37, p = 0.018), but positively with FSS in adults aged >52 years (β = 0.13, t = 2.51, p = 0.012). Longitudinal analysis demonstrated a similar pattern. <i>Conclusions:</i> Decreased cardiac vagal activity is associated with a higher number of FSS in adults aged ≤52 years in the general population. The unexpected association between increased cardiac vagal activity and FSS in adults aged >52 years needs further exploration. The role of age should be acknowledged in future studies on ANS function in the etiology of FSS.