Background: Fibromyalgia Syndrome (FMS) is a highly prevalent health problem whose main symptom is widespread pain, although it presents as other manifestations, such as loss of balance, that seem to mainly affect visuo-vestibular information. Objective: to compare the effects of a Vestibular Rehabilitation (VR) program versus those of a Conventional Physical Exercise (CPE) program on the health status of patients with FMS. Methods: A single-blind randomized controlled trial was performed. Patients with FMS were randomly assigned to VR or CPE programs. The protocols were performed in 40 min group sessions, twice weekly, for 16 sessions. Perceived health status, static and dynamic balance, verticality perception, confidence in balance, sensitization and kinesiophobia were measured at baseline, post-treatment and at the three-month follow-up and analyzed using an intention-to-treat approach. Results: Forty-eight subjects were randomly assigned, of whom thirty-five completed the planned VR (n = 19) or CPE (n = 16) program. At the three-month follow-up, there were differences in physical health status measured with the SF-12 (mean = −4.36, SE = 1.88, p = 0.027), balance during walking (mean = 1.90, SE = 0.57, p = 0.002), the perception of verticality in degrees (mean = 3.61, SE = 1.51, p = 0.024) and the anteroposterior position of the center of pressure (mean = −7.88, SE = 2.80, p = 0.009), as well as a decrease in the number of falls (mean = 0.98, SE = 0.44, p = 0.033), favoring the VR group. Conclusions: Vestibular Rehabilitation can be as beneficial as conventional exercise in improving the state of health in patients with Fibromyalgia Syndrome, providing additional improvements in physical health status, body balance, the perception of verticality and the number of falls.