Enterogenous cysts (ECs) are rare, inborn lesions of central nervous system, which mostly occurred in the ventral side of the spinal cord as well as common in children; adult intracranial cysts are rare. Although the morbidity of intracranial ECs is quite low, we also can make a preliminary diagnosis of those patients with the help of imaging examination. In this article, we introduced 1 case of ECs ventral to the brainstem, which present images on magnetic resonance imaging as hypointense lesions on T1-weighted and high-intensity mass on T2-weighted image. In consideration of the difficulty of the surgical approach and the surgical visual field exposure, we use microscope and nerve endoscope to design personalized surgical approach to minimize the surgical injury. Pathologic examination showed that it was typical EC. Not only is the location extremely rare, but also the surgical method is uncommon in this disease. We not only study the intracranial ECs’ manifestations, but also discuss the surgical approach and the application of nerve endoscope of our choice,which aims to provides a new surgical therapeutic approach for these lesions.