Paced breathing has shown efficacy in fibromyalgia (FM), but the mechanisms associated with symptom change are largely unknown. We investigated whether changes in respiratory rate (RR) alone resulted in autonomic changes during normal, paced, and mechanically assisted breathing in untrained FM patients and controls. Participants included 20 FM patients and 14 controls matched for age and body mass index. During a single visit, participants completed three 15-minute breathing sessions: 1) normal breathing, 2) slow-paced breathing, and 3) mechanically assisted breathing (continuous positive airway pressure) while supine. Continuous blood pressure and electrocardiogram were recorded, and measures of heart rate variability (HRV) and spontaneous baroreceptor sensitivity (sBRS) were calculated. During normal breathing, FM patients had higher heart rate (HR), but lower HRV and sBRS variables compared to controls with no difference in RR. Compared to the paced breathing condition, FM patients had significantly lower HR with higher HRV and sBRS variables during mechanically assisted breathing, despite no significant change in RR. Mechanically assisted breathing provided greater benefits in autonomic function than paced breathing in untrained FM patients. Future research will be needed to elucidate the central pathways involved in these autonomic changes and whether training in paced breathing can eventually replicate the results seen in mechanically assisted patients.