Hydroxysafflor yellow A (HSYA) is a main chemical component of the flower of Carthamus tinctorius. The present study investigated whether HSYA could attenuate brain injury induced by lymphostatic encephalopathy (LE). This was induced in adult male Wistar rats by cervical lymphatic blockade (CLB). Heart rate variability (HRV) was used as an indirect measurement of the regulatory function of the autonomic nervous system by recording the ECG signals from rats. It was shown that treatment with HSYA (5 mg/kg, i.p.) significantly alleviated the neurological deficits observed in rats with LE. Histological staining revealed that HSYA treatment attenuated LE-induced cell apoptosis in the rostral ventrolateral medullus (RVLM). Animals in the LE groups exhibited impaired regulatory roles of the autonomic nervous system in cardiovascular function, which was suppressed by pretreatment with HSYA. Additionally, HSYA administration significantly prevented the decrease of endothelial nitric oxide synthase (eNOS) mRNA and protein expression in the RVLM of rats with LE. These findings suggest that HSYA might provide neuroprotection against LE-induced brain injury and the associated functional alterations, which is likely regulated by the nitric oxide pathway.