BACKGROUND: Fibromyalgia is a syndrome of chronic, generalized muscular pain, accompanied by sleep disturbances, fatigue and cardic autonomic dysfunction that will affect the quality of life. There is currently no gold standard treatment. There are limitations of studies with electroacupuncture in auricular acupuncture. OBJECTIVES: We evaluate the effects of systemic electroacupuncture (EA) with frequencies of 2/100 Hz associated of auricular acupuncture with a Nogier frequency (2.28, 4.56 and 9.12 Hz) for pain intensity, heart rate variability (HRV), and quality of life in fibromyalgia. METHODS: Randomized clinical trial, a pilot study. Eighteen volunteers were randomized into a control group (CG, n = 9) and an experimental group (EG, n = 9). Six systemic EA sessions systemic and auricular were applied in the EG for 20 min, twice a week, for six weeks consecutive. The Numerical Pain Assessment Scale (NPRS), 2010 diagnostic criteria of the American College of Rheumatology (FDC 2010), Fibromyalgia Impact Questionnaire (FIQ) and analysis of HRV were the instruments used. The independent t-test compared to the groups was applied. RESULTS: There was no statistically significant difference for the primary outcome for NPRS (p > 0.05). In the secondary outcome there was a significant difference in the total score and in some FIQ domains (p = 0.008) and some variables such as pain (p = 0.02) and anxiety (p = 0.006). There was no significant difference for the FDC 2010 and HRV variables (p > 0.05). CONCLUSION: 2/100 Hz systemic EA associated with the Nogier frequency positively influenced some quality of life variables; however, pain intensity, diagnostic criteria, and HRV variables did not change.