Recent studies have suggested that maternally deprived rats exhibit anxiogenic-like behavior when exposed to stress in later life. Neuropeptide Y (NPY) is involved in the regulation of various physiological functions such as the expression of anxiety. Female Wistar rat pups were separated from their mothers for 3h daily from postnatal days 3 (P3) to 14 (P14). Acupuncture groups were treated with acupuncture at Shenmen (HT7) or Zusanli (ST36) on alternate days from P50 to P62. Their anxiety-like behavior was evaluated using an elevated plus-maze at P62, and then NPY immunohistochemistry in the basolateral amygdala (BLA) was performed. Rats exposed to maternal separation (MS) were less likely to explore the open arms of the plus-maze compared to control rats that were not exposed to MS. Among maternally separated groups, the percentage of time spent in the open arms was significantly increased in the HT7 acupuncture group, but not the ST36 acupuncture group, compared to MS group. In accordance with this behavior, the numbers of NPY-immunoreactive cells in the BLA were lower in the MS group compared to the control group. Among maternally separated groups, the numbers of NPY-immunoreactive cells in the BLA were significantly higher in the HT7 acupuncture group, but not higher in the ST36 acupuncture group, compared to MS group. These findings suggest that acupuncture treatment might reduce anxiety-like behavior in adult rats following maternal separation by modulating the NPY system in the amygdala.