ZAP-70 deficiency is a rare primary immunodeficiency disorder characterized by a severe defect in T-cell receptor signaling, leading to impaired immune function. Early diagnosis and intervention play a crucial role in preventing life-threatening infections and improving patient outcomes. We presented a case involving a novel mutation in the ZAP 70 gene, presented with Burkholderia cepacia, an uncommon pathogen. Immunological assessment guided genetic testing, which confirmed the diagnosis through the identification of a novel homozygous missense mutation in the ZP 70 gene.