The present invention relates to a composition comprising a cell permeable nucleic acid complex as an active ingredient for preventing or treating rheumatoid arthritis and, more specifically, to a pharmaceutical composition for preventing, alleviating, or treating rheumatoid arthritis, the composition comprising a cell permeable nucleic acid complex in which a bioactive nucleic acid targeting a JAK1 gene or a JAK2 gene is complementarily coupled with a carrier peptide nucleic acid. The cell permeable nucleic acid complex in which a bioactive nucleic acid targeting a JAK1 gene or a JAK2 gene is complementarily coupled with a carrier peptide nucleic acid according to the present invention, has high cell permeability and as such, inhibits the expression of a JAK1 gene or a JAK2 gene even without direct injection and thereby is useful for preventing, alleviating, or treating rheumatoid arthritis.