The invention relates to a method of treating chronic granulomatous disease through Hematopoietic stem cell (HSC) transplantation. The method comprises the steps of administering stem cell mobilization agent to human such that the target stem cell population migrates from host niches into the subject's blood. The target stem cells are removed from blood and administering the therapeutic stem cells to human and said therapeutic stem cells are engineered to express gp91phox. The steps are repeated multiple times i.e. at least four times. The mobilization agents used in the invention are granulocyte-colony stimulating factor and AMD3100. The method of HSC transplantation is effective in treatment of chronic granulomatous disease.