Sepsis is a life-threatening condition caused by the inflammatory response to invading organisms. Polymyxin B-immobilized fiber column direct hemoperfusion (PMX-DHP) is used to reduce blood endotoxin levels and modulate circulating inflammatory cytokine levels in sepsis patients. Here we report that severe sepsis caused by an infection of the gram-negative bacterium Pantoea agglomerans in a patient with small cell lung carcinoma was treated successfully with antibiotics and PMX-DHP. The patient, a 49-year-old Japanese male smoker whose condition was complicated with hyponatremia due to SIADH (syndrome of inappropriate secretion of antidiuretic hormone), rapidly developed sepsis and disseminated intravascular coagulation (DIC) after the administration of cisplatin and irinotecan. Despite initial antibiotics therapy, severe host responses including hypotension, high body temperature and tachycardia were noted. We initiated PMX-DHP, and the patient's Sequential Organ Failure Assessment score was greatly reduced and his DIC improved immediately. To our knowledge, this is the first reported case of PMX-DHP therapy for severe sepsis caused by P. agglomerans infection. Although the efficacy of PMX-DHP in sepsis is not well defined, PMX-DHP therapy should be considered in cases of sepsis from gram-negative infections.