Congenital spinal intradural arachnoid cyst associated with intrathoracic meningocele is very rare. We report a case in a 9-year-old Chinese boy who presented with a two-week history of progressive paraparesis and gait ataxia. Magnetic resonance imaging revealed that a dorsal intradural extramedullary cystic lesion extended from T1 to T5 and compressed the spinal cord. A left lateral intrathoracic meningocele pouch was found incidentally at the level of T1. The arachnoid cyst as well as meningocele was removed and the spinal cord compression was relieved. Arachnoid cyst was confirmed by histological examination. The patient recovered well postoperatively. This is the second report of such a case in the world according to the available literature. The take-home message for our case is that the surgical approach should be individualized, depending on the size and location.