Cardiac autonomic dysfunction has been reported in patients with cerebral palsy (CP). The aim of this study was to assess the existing literature on heart rate variability (HRV) in pediatric patients with CP and a special attention was paid to the compliance of the studies with the current HRV assessment and interpretation guidelines. A systematic review was performed in PubMed, Web of Science, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) databases searched for English language publications from 1996 to 2019 using Medical Subject Headings (MeSH) terms “heart rate variability” and “cerebral palsy” in conjunction with additional inclusion criteria: studies limited to humans in the age range of 0–18 years and empirical investigations. Out of 47 studies, 12 were included in the review. Pediatric patients with CP presented a significantly higher resting heart rate and reduced HRV, different autonomic responses to movement stimuli compared to children with normal development, but also reduced HRV parameters in the children dependent on adult assistance for mobility compared to those generally independent. None of the included studies contained the necessary details concerning RR intervals acquisition and HRV measurements as recommended by the guidelines. Authors of HRV studies should follow the methodological guidelines and recommendations on HRV measurement, because such an approach may allow a direct comparison of their results.