The aim of this study was to provide a novel insight into the mechanism of how medial prefrontal cortex (mPFC) participates in Post-Traumatic Stress Disorder (PTSD) by investigating the level of caspase- 3 and 9 in mPFC of Single Prolonged Stress (SPS) rats. A total of 100 male Wistar rats were randomly divided into a normal control group and SPS groups with 1, 4, 7 and 14 days of treatment. The PTSD model was created by SPS. The expressions of caspase-3 in SPS groups were significantly increased, compared with normal control group (P<0.05), and peaked at 7 days after exposure to SPS. In normal control group, the fluorescent intensity of caspase-9 positive cells was poor, and that of SPS groups was significantly stronger than normal control group (P<0.01), and peaked at 4 day after exposure to SPS. After SPS stimulation, caspase-3 and caspase-9 mRNA levels gradually increased, compared with control group, and peaked with 7 and 4 days of treatment, respectively (P<0.01). These results reveal that caspase-9 and caspase-3 may play an important role in the pathology of PTSD, which provides experimental evidence for the pathogenesis of PTSD.