Spontaneous intracranial hypotension in childhood is rare, and a few cases have been reported as a cause of headache in children. A 9-year-old boy was admitted to our hospital with a 3-day history of new-onset headache that worsened upon standing or walking, and aggravating low back pain. No medical history of injury, connective tissue disorder or migraine was detected. A neurological examination revealed neck stiffness. His initial blood tests suggested acute kidney injury by increased blood urea nitrogen (BUN) and creatinine. Brain computed tomography (CT) and cerebral spinal fluid (CSF) analysis were normal: however, opening pressure was low (< 60 mm H₂O). Magnetic resonance imaging (MRI) of the spine showed a collection of cerebral spinal fluid in the dorsal extradural space throughout the entire thoracic and lumbar spine level. The patient was diagnosed as having spontaneous intracranial hypotension accompanied by acute kidney injury. Magnetic resonance myelography and spinal MRI performed 14 days later did not show any cerebrospinal fluid leak. The headache and back pain were alleviated with strict bed rest and hydration. He remained free of headache and back pain at the 2-month follow-up. Here, we report a case of a 9-year-old boy with spontaneous intracranial hypotension.