Muscle atrophy is one of the serious complications in lower paraplegias of both central and peripheral types, which complicates the recovery of motor function in patients with spinal cord injuries. Traditional treatment and rehabilitation methods do not always yield positive results, making the study of the effectiveness of complex magnetic stimulation a relevant task. The study involved 30 patients with spinal cord contusions, divided into two groups: the study group (with the use of complex magnetic stimulation) and the control group (without stimulation). The therapy course lasted 65.7 ± 26.4 days. Complex magnetic stimulation included transcranial, segmental, and peripheral stimulation aimed at preventing muscle atrophy and improving motor function. The efficacy of the therapy was assessed based on changes in thigh and calf circumference and motor activity using the ASIA scale. The results showed statistically significant improvements in the study group, including an increase in thigh and calf circumference (p < 0.05), while no such changes were observed in the control group. The evaluation of motor activity did not show statistically significant differences between the study and control groups. Thus, complex magnetic stimulation may be an effective method of combating muscle atrophy and can be recommended for use in comprehensive rehabilitation programs for patients with lower paraplegia. Further studies with larger patient samples and new assessment criteria are required to better understand the impact of magnetic stimulation on therapy effectiveness in patients with central and peripheral lower paraplegias.