Purpose The exact risk of type 2 diabetes mellitus (T2DM) in women with polycystic ovary syndrome (PCOS) is unknown. It is also unclear if obesity independently increases T2DM risk in this population. The aim of this study was to systematically review and synthesize the best available evidence regarding the association between PCOS and T2DM, stratified according to obesity status. Methods A comprehensive search was conducted in PubMed, CENTRAL and Scopus databases up to October 31, 2020. Data are expressed as relative risk (RR) with 95% confidence interval (CI). The I 2 index was employed for heterogeneity. Results The eligibility criteria were fulfilled by 23 studies (319,780 participants; 60,336 PCOS and 8847 type 2 diabetes cases). Women with PCOS demonstrated a higher risk of T2DM than those without PCOS (RR 3.45, 95% CI, 2.95–4.05, p  < 0.001; I 2 81.6%). This risk remained significant both in studies matched or unmatched for participants’ age. With regard to body mass index (BMI), the RR for developing T2DM in obese and non-obese PCOS women compared with their non-PCOS counterparts was 3.24 (95% CI 2.25–4.65; p  < 0.001; I 2 30.9%) and 1.62 (95% CI 0.14–18.50; p  = 0.70; I 2 89.9%), respectively. The RR for developing T2DM was 3.85 (95% CI 1.99–7.43; p  < 0.001; I 2 46.2%) in obese compared with non-obese women with PCOS. This was also the case for overweight compared with lean women with PCOS. Conclusions Women with PCOS present an increased risk of T2DM compared with non-PCOS women only if they are obese/overweight.