<p>Neonatal hypoxic-ischemic encephalopathy (HIE) affects approximately 0.2%–0.3% of live births in developed countries, and nearly 40% of survivors experience lasting cognitive impairments, often accompanied by circadian rhythm disturbances. To explore the underlying mechanism, we examined the expression changes of miR-9a-5p in a neonatal rat model of hypoxic-ischemic brain damage (HIBD) and assessed its long-term influence on circadian rhythm and cognitive function. The results show that miR-9a-5p is significantly upregulated in the pineal gland of HIBD rats. Dual-luciferase reporter experiments further confirm that miR-9a-5p directly targets Clock. Compared with sham-operated controls, HIBD rats showed a significant reduction in the transcript levels of Clock and other circadian genes, including Per1, Cry1, and Bmal1. Behavioral analyses demonstrated that overexpression of miR-9a-5p disrupted circadian rhythm, accelerating the onset of physical activity. Furthermore, performance in the Morris water maze, open field, and novel object recognition tests indicated that miR-9a-5p overexpression significantly impaired cognitive function and increased anxiety-like behaviors. These findings suggest that miR-9a-5p exerts notable pathological effects in the HIBD model by targeting Clock, and the circadian rhythm genes it regulates may serve as potential therapeutic targets for circadian rhythm-related cognitive dysfunction following HIBD.</p> Graphical abstract <p>Schematic diagram illustrating the mechanism by which miR-9a-5p influences circadian rhythm and neurobehavioral outcomes in HIBD through the regulation of the Clock gene.</p> <p></p>