Post-traumatic stress disorder (PTSD) is the serious psychiatric disorder. Paeoniflorin (PF) produces the antidepressant-like properties. However, few studies are concerned about its anti-PTSD-like effects and mechanisms. To investigate these, the single prolonged stress (SPS) model was utilized. PTSD-like behavioral deficits in rats after exposure to SPS were improved by PF (10 and 20 mg/kg, i.p.), evidenced by blocking increased freezing time in contextual fear paradigm (CFP) and increased time and entries in open arms in elevated plus maze (EPM) test without affecting the locomotor activity in open field (OF) test. We also found that increased levels of corticosterone (Cort), corticotropin releasing hormone (CRH) and adrenocorticotropic hormone (ACTH) after exposure to SPS were reversed by PF (10 and 20 mg/kg, i.p.) in serum, respectively. Moreover, the decreased levels of serotonin (5-HT) and 5-Hydroxyindoleacetic acid (5-HIAA) in prefrontal cortex and hippocampus were reversed by PF (10 and 20 mg/kg, i.p.), respectively. In summary, the anti-PTSD-like activities of PF were associated with the modulation of HPA axis and 5-HT system activation.