Polycystic ovary syndrome (PCOS) is one of the most prevalent reproductive disorders in women worldwide. Despite rigorous research, the exact molecular mechanism that governs PCOS pathogenesis remains unclear. To investigate the potential roles of circular RNAs (circRNAs), this study sequenced ribosomal RNA‐depleted total RNA from exosomes of follicle fluids obtained from PCOS patients using non‐PCOS samples as controls. Bioinformatic analysis identified 167 upregulated and 245 downregulated circRNAs from a total of 16,771 detected candidates. Functional analysis suggests that pathways related to bacterial infection, associated chronic inflammation, and oxidative stress could be targeted by the differential circRNAs in PCOS patients. The obtained sequencing results were further validated by quantitative reverse‐transcription polymerase chain reaction and a circRNA–microRNA interaction network was constructed. The obtained results provide a valuable addition to the published studies on the mechanism of PCOS pathogenesis by revealing a wide variety of new circRNAs, miRNA, and gene targets that merit further investigation. We have provided the first study on the dysregulation of circRNAs in patients with polycystic ovary syndrome using RNA sequencing and bioinformatic analysis. We identified over 16,771 differentially expressed circRNA candidates, many of which showed implication in pathological processes such as bacterial infection, oxidative stress, and autophagy.