CD4⁺ 25⁺ regulatory T cells (Tregs) play a role in controlling the development and progression of autoimmunity. The transcription factors Foxp3 and NFATC2 (NFAT1) play key roles in regulating the development and function of Tregs. The present study examined the involvement of Tregs in the pathophysiology of autoimmune neutropenia in children. Tregs were analysed by flow cytometry, based on the expressions of CD4, CD25, and intracellular Foxp3. The expressions of FOXP3 and NFATC2 mRNA in the CD4⁺ 25⁺ cells were determined by quantitative real‐time polymerase chain reaction. The percentage of CD4⁺ 25^high Tregs in patients with autoimmune neutropenia was significantly lower than that in age‐matched healthy subjects. The intracellular expression of Foxp3 of CD4⁺ 25⁺ cells in patients similarly decreased in comparison to that in healthy subjects. The expression of FOXP3 and NFATC2 mRNA of CD4⁺ 25⁺ cells in patients also significantly decreased in comparison to that in healthy subjects. These results suggest that the deficiency of Tregs might thus play an important role in the immunopathophysiology of autoimmune neutropenia in children.