A 24-year-old man, who had an asymptomatic septum pellucidum cyst incidentally found one year previously, presented with severe headache and right abducens nerve palsy caused by expansion of the midline cyst. Preoperative magnetic resonance (MR) imaging revealed obstructive hydrocephalus due to the enlarged midline cyst. Neuroendoscopic fenestration of the septum pellucidum cyst was successfully performed via a right frontal approach using a high-resolution flexible neuroendoscopic system without complication. Communication between the cyst cavity and bilateral lateral ventricles was constructed via a single trajectory. The entire inner cyst wall could be inspected from the cyst cavity by manipulating the flexible neuroendoscopic system, which excluded the presence of neoplasm. His symptoms were completely relieved after surgery, and postoperative MR imaging showed significant improvement of hydrocephalus and shrinkage of the midline cyst. Septum pellucidum cavum vergae cyst may expand and become symptomatic, so fenestration using a flexible neuroendoscope system may be the optimal method for constructing communication to the bilateral lateral ventricles with minimal invasion.