Valerian root is the most commonly used herbal supplement for sedation and anxiolysis, but it is unknown whether it may affect functional brain connectivity. Our goal was to use electroencephalography (EEG) to investigate whether valerian root extract (VRE) affects resting-state connectivity changes and whether such changes are associated with clinical symptoms. This 4-week, double-blinded, randomized, placebo-controlled clinical trial was conducted with 64 nonclinical volunteers suffering psychological stress. The participants received VRE (100 mg) or a placebo thrice daily. We examined VRE's therapeutic effects on anxiety and stress-related psychological constructs. Functional brain connectivity changes were measured as EEG coherence in the alpha and theta frequency bands. The VRE and placebo groups both exhibited significant postintervention improvements on all clinical scales, but no significant between-group differences in these changes were noted. Compared with the placebo group, the VRE group exhibited significantly greater increases in frontal brain region alpha coherence across four electrode pairs, and these changes were significantly correlated with anxiolysis. The VRE group also exhibited significantly greater decreases in theta coherence across another four electrodes pairs. Our findings indicate that VRE alters functional brain connectivity in relation to anxiety. Further EEG studies are needed to confirm VRE's neurophysiological effects.