Anaesthesia exposure causes changes in the developing brain and affects behaviour and memory. This study examined the beneficial effect of pachypodol against isoflurane (ISF)-induced neuronal injury. Seven-day old rats were treated with 10 mg/kg and 30 mg/kg intravenous pachypodol 30 min before exposure to ISF (0.75%) for 6 h. Oxidative stress and other biochemical parameters were assessed in the brain tissue and serum using enzyme-linked immunosorbent assay. Additionally, a TUNEL assay was performed to assess neuronal cell apoptosis in several regions of the hippocampus. Cognitive function and neurological scores were determined in the pachypodol-treated neuron-injured rats. Cytokine levels and oxidative stress were reduced in the pachypodol-treated group compared to the ISF group. In addition, cognitive deterioration was reversed in pachypodol-treated compared with ISF-treated rats. Thus, treatment with pachypodol reduced neuronal apoptosis in neuron-injured rats. Moreover, pachypodol ameliorated changes to the JNK/ERK/Akt pathway in brain-injured rats. In conclusion, pachypodol treatment prevents neuronal apoptosis in ISF-treated rats by regulating the JNK/ERK pathway.