Spontaneous intracranial hypotension (SIH) is a well-established condition typically presenting with disabling orthostatic headache. Corpus callosum agenesis (CCA) is one of the most common human brain malformations with a wide spectrum of associated malformations, chromosomal abnormalities, and clinical syndromes. A 53-year-old woman presented with recurrent orthostatic headache for about 1 month. The head computed tomography examination of the patient showed CCA and the initial pressure of subsequent lumbar puncture was only 5 centimeters cerebrospinal fluid. Magnetic resonance imaging examination confirmed CCA with gray matter heterotopia. The final diagnose was SIH related headache with CCA. The patient's symptom improved after oral hydration, intravenous fluids, and bed rest. Favorable outcome was observed. Although this co-occurrence of SIH and CCA is probably coincidental, this finding suggests that the developmental malformations of the brain may lead to structural changes in brain tissue or disturbances in cerebrospinal fluid production and reflux, resulting in pathological changes over time.