Background: Over the decades, studies from various populations have found fibromyalgia and dysautonomia to be linked. However, recent evidence from Indian populations contradicts these findings. Methods: This cross-sectional study, conducted in a quaternary care centre in South India, recruited 30 women with fibromyalgia (2016 ACR criteria) and 30 age and sex-matched controls. We assessed all participants using Composite Autonomic Symptom Score (COMPASS-31) questionnaires, Sympathetic Skin Response (SSR) for sympathetic dysfunction and Heart Rate Variability battery of tests for parasympathetic dysfunction. Results: Median age of the women was 40 years. Fibromyalgia group reported severe levels of pain and disease impact on life. Fourteen participants (46.7%) with fibromyalgia tested positive for either sympathetic or parasympathetic dysfunction or both, while none of the control participants tested positive for either (odds ratio [OR] = 53.6, 95% confidence interval [CI] = 3–957, p = 0.0068). Conclusion: Dysautonomia is strongly associated with fibromyalgia syndrome. Further research is needed to determine causality.