A 23-year-old woman was injured in a rear-end collision. She had general malaise and posterior neck pain, which were more severe when she was in an upright position. Magnetic resonance imaging (MRI) revealed the presence of cerebellar tonsil descensus and syringomyelia in the spinal cord. Radioisotope (RI) cisternography showed signs of an early accumulation of RI in the bladder, and a delayed accumulation of RI in the cerebral fornix. We considered the possibilities of cerebrospinal fluid (CSF) hypovolemia and congenital Chiari type-1 malformation as being responsible for her headache. To obtain a definitive diagnosis, we performed gadolinium (Gd)-enhanced MR cisternography and found evidence of CSF leakage. We performed an epidural blood patch (EBP), and her symptoms resolved. In 2 years since the episode, her symptoms have not recurred, and additional treatment has not been required. In addition, MRI performed 2 years after the EBP did not reveal any changes. There seems no previous report which described successful differentiation of pre-existing congenital Chiari type-1 malformation from the acquired one caused by symptomatic CSF hypovolemia. Because treatment protocols differ between these two conditions, the establishment of a correct diagnosis is important.