We report a case of a four-year-old male who presented with symptoms of brainstem compression and lower cranial nerve neuropathies. MRI revealed a large, pre-pontine mass causing brainstem compression with an uncertain intra-axial component. Using diffusion tensor imaging (DTI) tractography and other imaging modalities, we were able to confirm that the lesion was extra-axial and did not involve the corticospinal tracts. In addition, DTI tractography illustrated that corticospinal tracts were displaced to the right obligating a left-sided approach. Upon resection, the mass was identified as a pre-pontine, extra-axial neurenteric cyst (NEC), which represents a rare finding in the pediatric population. The patient ultimately did well following the drainage and resection of the cyst wall and had excellent recovery. In this paper, we discuss the pathophysiology of and treatment options for NECs and explain how DTI tractography in our case assisted in planning the surgical approach.