We present a case of disseminated granulomatous disease associated with live attenuated vaccine-derived rubella virus (VDRV) in an immunodeficient patient who subsequently developed fatal multi-organ failure, including neurological deficits, with VDRV detected in the cerebrospinal fluid. Posthumous genetic analysis found a heterozygous missense mutation in IKZF3, a gene where haploinsufficiency is linked to immunodeficiency and immune dysregulation. Functional studies demonstrated that this mutation decreases AIOLOS protein stability and half-life, and family members carrying the same mutation exhibited decreased AIOLOS levels. This report underscores the importance of considering persistent rubella virus (RuV) infection in patients with cutaneous granulomatous lesions and highlights the need for comprehensive evaluation to uncover potential underlying immunodeficiencies, which could inform and optimize individualized treatment strategies.