Functional gastrointestinal disorders (FGID) and gastroesophageal reflux (GERD) disease affect a large global population and incur substantial health care costs. Impairment in gut-brain communication is one of the main causes of these disorders. The central nervous system (CNS) provides its inputs to the enteric nervous system (ENS) by modulating the autonomic nervous system (ANS) to control the gastrointestinal functions. Therefore, GERD and FGID’s might be associated with autonomic dysfunction, which can be identified via heart rate variability (HRV). FGIDs may be treated by restoring the autonomic dysfunction via neuromodulation. This article reviews the roles of HRV in the assessment of autonomic function and dysfunction in (i) gastroesophageal reflux (GERD), and the following FGIDs: (ii) functional dyspepsia (FD) and gastroparesis, (iii) irritable bowel syndrome (IBS) and (iv) constipation. The roles of HRV in the assessment of autonomic responses to various interventions were also reviewed. We used PUBMED, Web of Science, Elsevier/Science direct and Scopus to search the eligible studies for each disorder, which also included the keyword ‘heart rate variability’. The retrieved studies were screened and filtered to identify the most suitable studies using HRV parameters to associate the autonomic function with any of the above disorders. Studies involving both human and animal models were included. Based on analyses of HRV, GERD as well as the FGIDs were found to be associated with decreased parasympathetic activity and increased sympathetic nervous system activity with the autonomic balance shifted towards the sympathetic nervous system. In addition, the HRV methods were also reported to be able to assess the autonomic responses to various interventions (mostly neuromodulation), typically the enhancement of parasympathetic activity. In summary, GERD and FGIDs are associated with impaired autonomic dysfunction, mainly due to suppressed vagal and overactive sympathetic tone, which can be assessed noninvasively using HRV.