Melatonin has been reported to regulate circadian rhythms and have anti‐inflammatory characteristics in various inflammatory autoimmune diseases, but its effects in diseases‐associated muscle atrophy remain controversial. This study is aimed to determine the evidence of melatonin in rheumatoid arthritis (RA)‐related pathological muscle atrophy. We used initially bioinformatics results to show that melatonin regulated significantly the correlation between pro‐inflammation and myogenesis in RA synovial fibroblasts (RASF) and myoblasts. The conditioned medium (CM) from melatonin‐treated RASF was incubated in myoblasts with growth medium and differentiated medium to investigate the markers of pro‐inflammation, atrophy, and myogenesis. We found that melatonin regulated RASF CM‐induced pathological muscle pro‐inflammation and atrophy in myoblasts and differentiated myocytes through NF‐κB signaling pathways. We also showed for the first time that miR‐30c‐1‐3p is negatively regulated by three inflammatory cytokines in human RASF, which is associated with murine‐differentiated myocytes. Importantly, oral administration with melatonin in a collagen‐induced arthritis (CIA) mouse model also significantly improved arthritic swelling, hind limb grip strength as well as pathological muscle atrophy. In conclusion, our study is the first to demonstrate not only the underlying mechanism whereby melatonin decreases pro‐inflammation in RA‐induced pathological muscle atrophy but also increases myogenesis in myoblasts and differentiated myocytes.