Background <p>Type 2 diabetes mellitus (T2DM) is associated with an increased risk of cognitive decline and neurodegenerative changes. Understanding structural brain changes in T2DM patients is crucial for developing targeted interventions.</p> Methods <p>This study adheres to the PRISMA guidelines and is registered on PROSPERO (CRD420251056572). Coordinate-based meta-analysis (CBMA) was used via seed-based d-mapping (SDM) technique to analyze cortical thickness (CTh) variations between T2DM patients and healthy controls (HC). Data were retrieved from PubMed and Web of Science up to April 30, 2025, using pre-specified inclusion and exclusion criteria.</p> Results <p>Significant CTh reductions were detected in the right rolandic operculum (ROL) and left superior temporal gyrus (STG) in T2DM patients. Jackknife analyses confirmed the robustness of these findings. Meta-regression suggested a negative association between BMI and CTh in these two regions, indicating that elevated BMI is associated with more pronounced cortical thinning.</p> Conclusion <p>Our study highlights specific brain regions impacted by T2DM, suggesting that neurodegenerative mechanisms and clinical correlates are involved. These findings highlight the necessity for integrated metabolic and neurological strategies for T2DM management.</p> Clinical trial number <p>Not applicable.</p>