Abstract Objective: Autonomic dysfunction is an important mechanism that could explain many symptoms observed in fibromyalgia (FM). Exercise is an effective treatment, with benefits potentially mediated through changes in autonomic modulation. Strengthening is one of the less studied exercises in FM, and the acute and chronic effects of strengthening on the autonomic system remain unknown. The objective of this study is to assess the effects of strengthening exercises (STRE) on autonomic modulation, pain perception and the quality of life (QOL) of FM patients. Methods: Sedentary women with FM (ACR 1990) will be randomly selected to STRE or flexibility (FLEX) exercises in a blind controlled trial. The intensity of STRE will be set at 45% of the estimated load of 1 Repetition Maximum (RM) in 12 different exercises. The primary outcomes will be pain measured using the Visual Analog Scale (VAS) and the Heart Rate Variability (HRV) analysis. Other outcomes will be assess: fitness measured by treadmill test, the sit and reach test (Wells and Dillon's Bench), handgrip dynamometry; and quality of life by the Fibromyalgia Impact Questionnaire (FIQ), the Beck and Idate Trait-State Inventory (IDATE), a short-form health survey (SF-36). Statistical analyses and ethical procedures: The visual analog scale (VAS) for pain will be the primary measure used to determine sample size. Statistical significance will be set at 5% and power of 80%. These led to at least 58 participants to be randomized. The main hypothesis is that strengthening exercise is a better treatment than flexibility exercise to improve pain, HRV and quality of life. In all measures tested we will consider the null hypothesis (H0) as being the point of equality between groups tested and H1 the point of difference. Bilateral tests were carried out adopting a 5% level of significance. The normality of the results will be tested using the Shapiro-Wilk test. Student's "t"-test for paired samples will be used to perform intra-group comparisons at different times, when the data were normally distributed, and the nonparametric equivalent of Student's t-test (Wilcoxon test) will be used when the data show an asymmetrical distribution. To compare the data between the STRE and FLEX groups, ANOVA for repeated measures will be used, followed by post-hoc Bonferroni's test.