Patients with severe primary immunodeficiency are at risk for complications from live attenuated vaccines. Here, we report a case of a vaccine associated paralytic polio (VAPP) and Bacille Calmette-Guérin (BCG) disease in a 6-month-old girl with severe-combined immunodeficiency (SCID) due to homozygous recombinant activating gene 1 (RAG-1) deficiency. The patient was successfully treated with intravenous immunoglobulins and oral pocapavir for poliovirus, and anti-mycobacterial therapy for regional BCG disease, allowing stem cell transplant. Following transplantation, poliovirus type 3 with 13 mutations was detected from cerebrospinal fluid but not from stool, indicating ongoing viral evolution in the central nervous system despite pocapavir treatment. Clinical improvement and immune reconstitution allowed the patient to be successfully discharged with no further detection of poliovirus.