Background Functional training is an exercise program to enhance physical abilities such as balance, coordination, agility, and power. The effectiveness of functional training in enhancing physical fitness and motor skills has been established through its use in rehabilitation treatment and sports training. However, current systematic reviews have not considered the impact of functional training on fundamental motor skills. This review aimed to examine the effect of functional training on the fundamental motor skills of children.Methods Following PRISMA guidelines, a search was conducted in six databases: PubMed, Scopus, ProQuest, Web of Science, EBSCOhost, and SPORT Discus, from January 2000 to December 2021.Results The search yielded 1451 papers, of which only 24 satisfied all inclusion and exclusion criteria. Significant improvements were found in the three main areas of FMS, namely, locomotor skills (n = 15), balance skills (n = 9), and objective control skills (n = 2), as well as general physical fitness (n = 14).Conclusions This systematic review shows that functional training effectively improves children’s fundamental motor skills. It is in accordance with the scientific theory of functional training. Closed kinetic chain exercises connect joints and muscle groups to work together, making movement and training safer and more effective. Furthermore, the study outcomes provide valuable insight into the potential benefits of functional training for children. It may help inform physical education programs and provide guidance on how to best use functional training to enhance children’s fundamental motor skills.