Background: Chronic granulomatous disease (CGD) is a rare, potentially life-threatening primary immunodeficiency caused by defects in the NADPH oxidase complex, leading to impaired phagocytic function and recurrent bacterial and fungal infections. Neonatal onset is extremely uncommon and may present with atypical, severe manifestations.

Case Presentation: We report a male neonate presenting at 44 days of life with persistent fever, nasal regurgitation of feeds, severe perianal excoriation, and necrotic palatal ulceration. Laboratory evaluation revealed leukocytosis, elevated C-reactive protein, and blood cultures positive for Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. Galactomannan ELISA suggested concomitant Aspergillus infection despite a negative KOH mount. Dihydrorhodamine (DHR) assay demonstrated a markedly reduced neutrophil oxidative index (3.4%), confirming CGD. The patient was managed with targeted intravenous antibiotics, surgical debridement, and initiation of prophylactic cotrimoxazole.

Conclusion: This case illustrates an unusual neonatal presentation of CGD with extensive necrosis involving the hard palate, nasal septum, and perianal region, highlighting the heterogeneity and diagnostic challenges of early-onset disease. Prompt recognition via DHR assay is essential for timely prophylactic therapy and multidisciplinary management. Awareness of such atypical presentations may facilitate earlier diagnosis, guide intervention, and improve neonatal outcomes. Longitudinal studies are warranted to clarify prognostic implications and optimize management strategies in extremely early-onset CGD.