Background. Disorders of autonomic nervous system caused up to 80% of functional disorders. There is no information about the influence of magnetotherapy (MT) on the indicators of vegetative homeostasis, which disturbance is a cause of functional pathology. Objectives. The aim of the study is to investigate vegetative rehabilitation trend of MT in various initial conditions of functional-vegetative disorders. Methods. Functional-vegetative diagnostics method by V.G. Makats was chosen as a method of control of MT impact. The diagnostic complex BIOTEST-12M was a technical tool. 38 children of different age and gender treated in the Department of Physiotherapy of Vinnytsia Regional Children Clinical Hospital in 2016-2017 were involved in the research. The patients were divided into 7 groups according to the levels of functional vegetative homeostasis. Results. MT had a different effect on vegetative activity as well as systemic and functional dependence, according to the coefficient of functional vegetative homeostasis. The most positive effect was evidenced in a group with a significant parasympathicotonia (group 1). In the group with severe sympathicotonia (group 6) it had negative effect. There were no gender and age-related characteristic features of the influence of MT on the dispersion of vegetative levels. Conclusions. Rehabilitation expediency requires maintenance of functional vegetative homeostasis at the level of FcP-VB-FcS in conjunction with functional-vegetative diagnostics using the method of V.G. Makats. Magnetotherapy can be recommended to be used only for patients with significant and expressed parasympathicotonia.