Because the Bacillus Calmette-Guérin (BCG) prevents infants from contracting miliary tuberculosis and tuberculosis meningitis, BCG vaccination is recommended for those under 6 months old in Japan. Complications such as favorable local inflammatory reactions including redness, induration, and abscess formation may occur, but severe adverse effects such as osteomyelitis, periostitis, and disseminated BCG infection are generally rare. We report an 11-month-old boy with severe combined immunodeficiency dying of serious disseminated BCG infection despite anti-tuberculosis therapy and blood stem cell transplantation. He was vaccinated with disseminated BCG infection at 4 months before severe combined immunodeficiency diagnosis was confirmed by specific RD gene deletion based on allele-specific polymerase chain reaction. Although BCG is considered safe, we should keep in mind that subjects with immunological deficiency may suffer severe BCG complications.