Background: Several mutations have been described leading to impaired immunity in the IL-12/ IFN-γ axis and, they confer susceptibility to mycobacterial infections. One of the more serious clinical phenotypes is secondary to mutations at IFN-γ receptor 1 gene, characterized by an early onset and more severe disease. Case report: We present a 3-month-old female patient with systemic M. tuberculosis complex who has a homozygous mutation, it affects the splicing site at IFNGR1 c.201-1G> T. At time of this report, she is with antimycobacterial treatment in the protocol of pluripotent hematopoietic cell transplantation (TCHP).