Introduction: Severe congenital pancytopenia is a rare and life-threatening bone marrow failure syndrome presenting early in life with recurrent infections. Mutations in the CDC42 gene are increasingly recognized as a cause of immune dysregulation, hyperinflammation. However, therapeutic options remain poorly defined. Case presentation: Index patient is the first child born to non consanguineous parents,delivered at term by emergency lower segment caesarean section due to fetal distress. From day two of life,developed persistent severe pancytopenia, accompanied by fever and markedly elevated inflammatory markers. Managed as severe neonatal sepsis and transferredto lady ridge way hospital for further evaluation. Bone marrow examination revealed marked hypocellularity . Genetic testing identified a heterozygous pathogenic exon 6 mutation in CDC42.Later developed hemophagocytic lymphohistiocytosis. Multidisciplinary discussions considered hematopoietic stem cell transplantation ; however, no feasible transplant optionwas available. Despite intensive supportive care, the child succumbed to overwhelming sepsis. Conclusion: Case highlights the aggressive clinical course of CDC42 related congenitalpancytopenia complicated by secondary HLH and the diagnostic and therapeutic challenges associated.