Background: The main aim of this study was to assess the effects of repetitive-transcranial magnetic stimulation (rTMS) in patients with fibromyalgia (FMS). Methods: We systematically searched PubMed, PEDro, EMBASE, and CINAHL. Methodological quality was analyzed using the AMSTAR and ROBIS scales, and the strength of evidence was established according to the guidelines advisory committee grading criteria. A total of 11 systematic reviews were included. The assessed variables were pain intensity, depressive symptoms, anxiety, and general health. Results: Regarding pain intensity, it seems that high-frequency rTMS significantly reduces pain intensity at a 1-month follow-up when the primary motor cortex (M1) is stimulated. However, we cannot robustly conclude the same for low-frequency protocols. When we look at the combination of high and low-frequency rTMS, there seems to be a significant effect on pain intensity up to 1-week post-intervention, but after that point of follow-up, the results are controversial. Regarding depressive symptoms and anxiety, results showed that the effects of rTMS are almost non-existent. Finally, in regard to general health, results showed that rTMS caused significant post-intervention effects in a robust way. However, the results of the follow-ups are contradictory. Conclusions: The results obtained showed that high-frequency rTMS applied on the M1 showed some effect on the variable of pain intensity with a limited quality of evidence. Overall, rTMS was shown to be effective in improving general health with moderate quality of evidence. Finally, rTMS was not shown to be effective in managing depressive symptoms and anxiety with a limited to moderate quality of evidence. PROSPERO number: This review was previously registered in PROSPERO (CRD42023391032).