Topical therapy is usually of limited benefit in the treatment of severe atopic dermatitis (AD), and the need for a safe and effective systemic treatment may be required in certain cases especially in children. We evaluated the efficacy and safety of methotrexate and cyclosporine in the treatment of 40 children with severe AD. Patients were divided into two groups (each consisting of 20 patients); group A was treated with methotrexate (7.5 mg/week) while group B was treated with cyclosporine (2.5 mg/kg/day). The severity scoring for atopic dermatitis (SCORAD) was used to indicate efficacy of treatment. In group A, the mean SCORAD score at the beginning of the study was 57.90 ± 3.21 that was reduced at the end of the treatment period to reach 29.35 ± 6.32 with a mean absolute reduction of 26.25 ± 7.03. In group B, the mean SCORAD score was 56.54 ± 4.82 at the start of treatment and was 31.35 ± 8.89 at the end of 12 weeks of treatment. The mean absolute reduction was 25.02 ± 8.21. There was no statistically significant difference in the reduction of SCORAD score between both groups (P ± 0.93). Mild and temporary adverse effects were reported in some patients in both groups. Methotrexate or cyclosporine in low doses can be considered as effective, relatively safe, and well-tolerated treatments for severe AD in children.