Aquaporin 9 (AQP9), an aquaglyceroporin, is an important aquaporin in the brain. This study examined the expression patterns of AQP9 and p38 mitogen-activated protein kinases (MAPK) in ischaemic brains from rats with permanent middle cerebral artery occlusion (pMCAO) to elucidate the function and regulation of AQP9 after ischaemia. AQP9 was co-localised with glial fibrillary acidic protein-positive astrocytes and neuronal nuclei-positive neurons in rat brains. Expression of AQP9 increased continuously until 24 h after pMCAO in the ischaemic core region and the border region. Importantly, this increase in expression of AQP9 correlated with brain oedema. AQP9 expression was predominant in astrocytes within 3 h after pMCAO and then in neurons 6 h after pMCAO. Phosphorylated p38 MAPK was also induced in the ischaemic core region and the border region at different time points after pMCAO. Interestingly, intracerebroventricular injection of the p38 MAPK inhibitor SB203580 attenuated AQP9 expression after pMCAO. Taken together, these results indicate that dynamic changes in AQP9 expression, mediated in part via the p38 MAPK signal transduction pathway, may contribute to the development of cerebral oedema after brain ischaemia.