Recently, heart rate variability (HRV) level has been found to be a risk factor for female sexual dysfunction. Low HRV was a significant predictor of female sexual arousal dysfunction and overall sexual dysfunction. Building upon this finding, the present study examined whether differences in vagal activity between sexually functional and sexually dysfunctional women may be driving the association between low HRV and female sexual dysfunction. Specifically, respiratory sinus arrhythmia (RSA) was assessed before, during, and after physiological sexual arousal in 84 women, aged 18 to 47, to examine potential differences in vagal activity between sexually functional and sexually dysfunctional women. Significant differences in vagal activity between these two groups were observed (p =.02). These findings provide additional specificity to the recently established relationship between HRV and female sexual function while also proposing a mechanism to target during treatments for sexual dysfunction.