Idiopathic CD4+ lymphocytopenia (ICL) is a rare immunodeficiency disease with severe CD4 T-cell depletion, leading to serious opportunistic infections. The optimal treatment of ICL has not been determined, especially in severe form of the disease. Here, we report an eight-yr-old girl with ICL who was successfully treated with fludarabine-based conditioning HSCT. To the best of our knowledge, this is the first pediatric ICL case that was treated by HSCT. Allogeneic HSCT with a reduced intensity condition (RIC) regimen may be a feasible and curative treatment option in ICL patients with recurrent life-threatening complications.