Fibromyalgia (FM) is a central sensitization syndrome that is strongly associated with the cerebral cortex. This study used bidirectional two-sample Mendelian randomization (MR) analysis to investigate the bidirectional causality between FM and the cortical surface area and cortical thickness of 34 brain regions. Inverse variance weighted (IVW) was used as the primary method for this study, and sensitivity analyses further supported the results. The forward MR analysis revealed that genetically determined thinner cortical thickness in the parstriangularis (OR = 0.0567mm, PIVW = 0.0463), caudal middle frontal (OR = 0.0346mm, PIVW = 0.0433), and rostral middle frontal (OR = 0.0285mm, PIVW = 0.0463) was associated with FM. Additionally, a reduced genetically determined cortical surface area in the pericalcarine (OR = 0.9988mm2, PIVW = 0.0085) was associated with an increased risk of FM. Conversely, reverse MR indicated that FM was associated with cortical thickness in the caudal middle frontal region (β = -0.0035mm, PIVW = 0.0265), fusiform region (β = 0.0024mm, SE = 0.0012, PIVW = 0.0440), the cortical surface area in the supramarginal (β = -9.3938mm2, PIVW = 0.0132), and postcentral regions (β = -6.3137mm2, PIVW = 0.0360). Reduced cortical thickness in the caudal middle frontal gyrus is shown to have a significant relationship with FM prevalence in a bidirectional causal analysis.