Multiple sclerosis (MS) is a common autoimmune and neurodegenerative disease of the central nervous system. Serum levels of melatonin decrease in MS patients who are also at risk of osteoporosis. Procalcitonin (proCT) has been reported as a biomarker of systemic inflammation and autoimmune disease; however, its changes in MS patients have not been well explored. This study investigated, using ELISA, the clinical correlation between serum melatonin and proCT in MS patients. We then assessed the effect of melatonin (10 mg/kg) therapy on bone metabolism and osteoporosis in experimental autoimmune encephalomyelitis (EAE) model of MS and in MS patients. Data showed a significant increase (*P < 0.05) in serum levels of proCT in MS patients, inversely correlated (r  =  −0.945; P  =  0.0001) with melatonin levels, compared to healthy participants. On the other hand, melatonin therapy ameliorated EAE severity by significantly decreasing (*P < 0.05) mean clinical scores, compared to control EAE mice. In addition, serum levels of proCT significantly (**P < 0.01) increased in EAE mice, compared to controls, which was significantly (*P < 0.05) reduced by melatonin. Moreover, EAE‐induced decrease in 25‐hydroxyvitamin D, calcium, and osteocalcin (OCN) in EAE mice, compared to controls, was significantly (*P < 0.05) increased by melatonin. Finally, OCN serum levels were found to be significantly decreased (*P < 0.05) in MS patients, in comparison with controls. Taken together, we suggest that proCT could be used as a diagnostic biomarker in MS patients and that melatonin normalizes bone metabolites in MS. Further clinical and experimental investigations are needed to understand bone metabolism in MS.