Atopic dermatitis (AD) is a chronic relapsing eczematous skin disease, which primarily affects infants and young children. Due to the side effects of commonly used drugs for its treatment, the development of safer therapeutic strategies is needed. There are many reports on the topical use of marshmallow (Althaea officinalis) for a range of skin diseases in Persian medicine. The main aim of the present investigation was evaluating the efficacy of marshmallow in children with mild‐to‐moderate atopic dermatitis. Another aim of the study was screening the anti‐allergic and anti‐inflammatory potential of phytocomponents against target proteins, including TNF‐alpha, IL6, and PDEs A, B, and D enzymes with PDB IDs: 2AZ5, 1P9M, 3I8V, 4KP6, and 1Y2K, respectively, along with their respective standard ligands using computational docking analysis. A pilot clinical trial was designed to investigate the safety and efficacy of Althaea officinalis in children with AD. The diagnosis of AD was made according to the criteria of Hanifin and Rajka. Children between 3 months and 12 years old were participated in this trial and randomly allocated into two parallel intervention and control groups. The intervention group used Althaea officinalis 1% ointment while the positive control group used Hydrocortisone 1% ointment twice a day for a week and after that, three times per week for a period of 3 weeks. The severity of AD was measured using the SCORAD score at the end of each assessment visits. A total number of 22 patients completed the study. A significant decrease of the SCORAD score was observed in both groups. At the end of the study, this score change, which indicates the improvement of the patients was significantly higher in the intervention group in comparison to the baseline (p‐value = .015) and week 1 (p‐value = .018). In the docking analysis of the study, 33 phytochemical compounds were identified, which were docked into the active site of IL6, TNF‐alpha, and human PDE4 isoenzymes. Affinity toward the selected enzymes was significantly higher in glycosylated compounds. The results of this pilot study showed that the efficacy of Althaea officinalis 1% ointment in a decrease of disease severity is more than Hydrocortisone 1% in children with AD. However, further studies are needed to confirm this finding. Moreover, the docking analysis revealed that the inhibitory activity of compounds with free hydroxyl groups such as glycosylated compounds was better than others, probably due to the hydrogen bond interaction of hydroxyl groups of the ligands with the enzymes.