The positive effects of physical training on heart rate variability (HRV) in healthy adults are widely recognized; however, the responsiveness to training in healthy children has not yet been established. The aim of this study was to determine the influence of physical training on HRV in prepubertal healthy children. Systematic computerized searches were performed from 1950 to 2012 in the following databases: Medline, Embase, Cinahl, Lilacs, Scielo, SportDiscus, ProQuest; Web of Science; PEDro; Academic Search Premier and the Cochrane Library. The key words used were: heart rate variability, autonomic nervous system, exercise training, physical activity, continuous exercise, intermittent exercise, children, prepubescent, adolescents, and healthy. Although the database search initially identified 6,164 studies, after removing duplicates and excluding by title the number was 148, however, only 2 studies were included in this systematic review. The meta-analysis compared the experimental group (n = 29) with the control group (n = 28) for the HRV parameters: RR intervals, SDNN, RMSSD, pNN50, LF (log), HF (log), LF/HF and Total Power (log). The meta-analysis demonstrated similar HRV indices between both the experimental and control groups. In conclusion, the available results from randomized controlled trials do not support the hypothesis that physical training improves HRV in healthy children[AUQ2].