The aim of this study was to assess the changes in melatonin concentration under the influence of magnetic stimulation in men with low back pain. A total of 15 men were used in this study, divided into two groups. In Group 1, consisting of seven men, the M1P1 Viofor JPS program was used twice a day for 8 min, at 08:00 and 13:00. In Group 2, consisting of eight men, the M2P2 Viofor JPS program was used once a day for 12 min at 10:00. The application was subjected to the whole body of patients. The treatments in both groups lasted 3 weeks, for 5 days each week, with breaks on weekends. The diurnal melatonin profile was determined the day before exposure and the day after the last treatment, as well as at one-month follow-up. Blood samples were collected eight times a day. In both programs, magnetic stimulation did not reduce the nocturnal peak of melatonin concentration. After exposure, prolonged secretion of melatonin was observed until the morning hours. The impact of the magnetic field was maintained 1 month after the end of the application. The effect of the magnetic field was maintained for 1 month from the end of the application, which confirms the thesis about the occurrence of the phenomenon of biological hysteresis. The parameters of the magnetic fields, the application system, and the time and length of the application may affect the secretion of melatonin.