Gastrointestinal symptomatology is frequent among patients with fibromyalgia, which increases disease burden and lacks specific treatment, either pharmacological or non-pharmacological. We aimed to evaluate the efficacy and tolerability of a multi-strain probiotic, VSL#3®, for the treatment of fibromyalgia-associated gastrointestinal manifestations. This randomized, placebo-controlled trial included 12 weeks of probiotic or placebo treatment followed by 12 weeks of follow up. The primary outcome variable was the mean change from the baseline to the endpoint in the composite severity score of the three main gastrointestinal symptoms reported by patients with fibromyalgia (abdominal pain, abdominal bloating and meteorism). Secondary outcome variables were the severity of additional gastrointestinal symptoms, fibromyalgia severity, depression, sleep disturbance, health-related quality of life and patients’ overall impression of improvement. No differences were found between VSL#3® (n = 54) and the placebo (n = 56) in the primary outcome (estimated treatment difference: 1.1; 95% confidence interval [CI]: −2.1, 4.2; p = 0.501), or in any of the secondary outcomes. However, responders to VSL#3 were more likely to maintain any improvement during the follow-up period compared to responders in the placebo arm. Overall, VSL#3 tolerability was good. Our data could not demonstrate any beneficial effects of VSL#3® either on the composite score of severity of abdominal pain, bloating and meteorism or in any of the secondary outcome variables. More research is needed to elucidate specific factors that may predict a favourable response to treatment in patients with fibromyalgia.