Previous studies have shown that fibromyalgia syndrome (FMS) is associated with low level of physical activity and exercise, which may lead to an increased risk of osteoporosis. However, studies of bone mineral density (BMD) in fibromyalgia have shown conflicting results. Thus, we conducted a systematic review and meta-analysis to better characterize the association between FMS and BMD. A comprehensive search of the databases MEDLINE and EMBASE was performed from inception through May 2016. The inclusion criterion was the observational studies’ assessment of the association between fibromyalgia and bone mineral density in adult subjects. Fibromyalgia was diagnosed in accordance with the American College of Rheumatology criteria for the diagnosis of fibromyalgia syndrome. BMD was measured at the lumbar spine and femoral neck by dual-energy X-ray absorptiometry. Pooled mean difference (MD) of BMD at each site and 95% confidence interval (CI) were calculated using a random-effect, generic inverse variance method. The between-study heterogeneity of effect size was quantified using the Q statistic and I². Data were extracted from four observational studies involving 680 subjects. At lumbar spine (L2–L4), BMD is significantly decreased in patients with FMS compared with controls with pooled MD of −0.02 (95% CI −0.03 to −0.01, P value = 0.003, I² = 0%) (Fig. 1). At femoral neck, BMD is not significantly decreased in patients with FMS compared with controls with pooled MD of 0.01 (95% CI −0.02 to 0.01, P value = 0.23, I² = 0%) (Fig. 2). In this meta-analysis, we observe that BMD at lumbar spine is decreased in FMS compared with normal individuals. Patients with FMS should be assessed for risk of osteoporosis.