A 44-month-old boy with chronic granulomatous disease has been suffering from fever and skin rash for 7 days prior to admission. The blood culture obtained on admission revealed Salmonella enterica subspecies houtenae. He received intravenous ceftriaxone therapy during his hospital stay and oral cefixime after discharge. Unfortunately, the same symptoms recurred 2 weeks after discontinuing cefixime and the culture from the aspirate of a skin nodule yielded the same microorganism again. He received intravenous ceftriaxone therapy after readmission and became afebrile 3 days later. However, focal seizure was noted on the 14th day of hospitalization. Brain magnetic resonance imaging revealed multiple brain abscesses, and electroencephalogram showed epileptiform activity. The intravenous antimicrobial agents were continued for a total of 84 days and interferon-gamma was administered as adjunctive therapy. Finally, he recovered from brain abscesses without any neurologic sequel. It is suggested that an extended course of antimicrobial treatment is necessary for chronic granulomatous disease with pyogenic infection because of the defective intracellular killing ability.