Abstract Purpose 18F-FDG thyroid incidentaloma (TI) occurs in ~2% of PET/CT examinations with a cancer prevalence of up to 35–40%. Guidelines recommend fine-needle aspiration cytology (FNA) if a focal 18F-FDG TI corresponds to a sonographic nodule >1 cm. The aim of this systematic review and meta-analysis was to provide evidence-based data on the diagnostic distribution of 18F-FDG TIs in the six Bethesda systems for reporting thyroid cytopathology (BETHESDA) subcategories. Methods Original studies reporting 18F-FDG TIs and cytologically classified according to BETHESDA were included. Six separate meta-analyses were performed to obtain the pooled prevalence (95% confidence interval, 95% CI) of 18F-FDG TIs in the six BETHESDA subcategories. Results Fifteen studies were finally included. Nine studies were from Asian/Eastern and six from Western countries. FNA data according to BETHESDA was available in 2304 cases. The pooled prevalence of 18F-FDG TIs according to BETHESDA was BETHESDA I 10% (6–14), BETHESDA II 45% (37–53), BETHESDA III 8% (3–13), BETHESDA IV 8% (5–12), BETHESDA V 6% (4–9), BETHESDA VI 19% (13–25). A significantly different prevalence was found in the BETHESDA IV between Asian/Eastern (2%) and Western (19%) studies. Conclusion Two-thirds of focal 18F-FDG TIs undergoing FNA have either malignant (BETHESDA VI) or benign (BETHESDA II) cytology while a minority will have indeterminate (BETHESDA III or IV) FNA results. Significant differences between Asian/Eastern and Western studies are also present in the prevalence of indeterminate FNA results.