This study aimed to investigate changes of characteristics of neural stem cells (NSCs) in a neonatal rat with hypoxic-ischemic brain damage (HIBD) and provide effective method and time window for the treatment of hypoxic-ischemic encephalopathy (HIE). A total of 231 7-day-old neonatal SD rats were randomly divided into control, hypoxic and HIBD groups (n=77 per group). Each group was randomly divided into 7 subgroups according to the time of sacrifice. Immunohistochemistry analysis was performed to confirm the expression of Nestin and HE staining was performed to detect the pathological change of HIBD. NSCs were mainly distributed in hippocampus, ependyma of lateral ventricle, subventricular zone (SVZ), striatum and cortex in three groups, while NSCs in HIBD group presented a regional distribution. As compared with control and HIBD groups, the number of NSCs was higher in hypoxia group at the same time point from day 3 (P<0.05). There was no difference in the number of NSCs in control and HIBD group at the same time of sacrifice (P>0.05) except day 3. The similar tendency of the number of NSCs was observed in 3 groups. There was no difference in NSCs number at the same time of sacrifice among 3 groups within 3 days expect hypoxia group. After 3 days, there was a trend of decreased number of NSCs in 3 groups with extending time (P<0.05). NSCs existed in brain tissue with pathological changes in the rats with HIBD all the way, and NSCs could benefit from hypoxia in a certain time. © 2014, Scientific Publishers of India. All rights reserved.