Circular RNAs (circRNAs) participate in diverse biological processes. However, whether circRNAs exhibit distinct expression patterns under obstructive sleep apnea (OSA)-induced chronic intermittent hypoxia (CIH) remains unexplored. We conducted RNA sequencing to compare expression profiles between CIH rats (n = 4) and normoxic controls (n = 4), identifying differentially expressed (DE) circRNAs. After filtering candidate circRNAs, we validated their expression in four OSA patients and four controls using qRT-PCR. Principal component analysis (PCA) was employed to confirm the diagnostic potential of these circRNAs. The miRanda software predicted target microRNAs (miRNAs), and the circRNA-miRNA regulatory network was visualized using Cytoscape software. In total, we identified 43 DE circRNAs, primarily enriched in functions like protein binding, cytoskeleton organization, and supramolecular complexes. We selected eight DE circRNAs associated with CIH for validation in OSA patients (n = 4) and controls (n = 4), with five displaying significant expression differences. These eight circRNAs showed distinct expression patterns between CIH and control groups, suggesting potential utility in distinguishing CIH conditions. Notably, our analysis identified mir-466b-3p as associated with DE circRNAs in the context of CIH. In conclusion, this study described circRNA expression profiles in CIH rats and identified several circRNAs with altered expression in CIH conditions. These findings suggest areas for further research into the relationship between circRNA expression and CIH.