Neurogenic bowel dysfunction (NBD) is a common problem for people with spinal cord injury (SCI) and multiple sclerosis (MS), which seriously impacts quality of life. Pharmacological management is an important component of conservative bowel management. The objective of this study was to first assemble a list of pharmacological agents (medications and medicated suppositories) used in current practice. Second, we systematically examined the current literature on pharmacological agents to manage neurogenic bowel dysfunction of individuals specifically with SCI or MS. We searched Medline, EMBASE and CINAHL databases up to June 2020. We used the GRADE System to provide a systematic approach for evaluating the evidence. Twenty-eight studies were included in the review. We found a stark discrepancy between the large number of agents currently prescribed and a very limited amount of literature. While there was a small amount of literature in SCI, there was little to no literature available for MS. There was low-quality evidence supporting rectal medications, which are a key component of conservative bowel care in SCI. Based on the findings of the literature and the clinical experience of the authors, we have provided clinical insights on proposed treatments and medications in the form of three case study examples on patients with SCI or MS.