Pancytopenia as a presenting feature of an Inborn Error of Metabolism (IEM) is rare. Two children with pancytopenia mimicking sepsis are presented here. Investigations revealed pancytopenia and metabolic acidosis. Both had previous episodes of encephalopathy. In view of the persisting pancytopenia, episodic encephalopathy and metabolic acidosis, despite therapy for sepsis, an underlying IEM was considered and further workup revealed organic acidemia. Both children were started on dietary modifications and supplements, to which they responded, however one of them succumbed to an intercurrent infection. IEM should be considered in children with episodic encephalopathy, metabolic acidosis and pancytopenia after ruling out sepsis. Timely intervention can reduce morbidity and mortality.