Peritoneal dialysis (PD)-associated peritonitis is a common complication of PD. Enteric peritonitis is defined as peritonitis arising from an intestinal or intra-abdominal organ source. The delay in the diagnosis or treatment of enteric peritonitis has been reported to increase mortality. Therefore, the early consideration of enteric peritonitis, particularly in cases of culture-negative peritonitis, is imperative. A 67-year-old Japanese man who had been undergoing PD for 3 years, was admitted to our hospital with a diagnosis of PD-associated peritonitis. A month previously, he experienced a bleeding gastric ulcer, which led to severe anemia (hemoglobin 6.3 mg/dL), followed by thrombocytosis. On admission, peritoneal fluid analysis showed a high white blood cell count (WBC: 8,570 /µL), with neutrophils predominating (74.5%). Cultures of both his dialysis effluent and blood were negative. After admission, the WBC count of the dialysis effluent gradually decreased alongside antibiotic therapy, but the patient’s abdominal pain did not improve. After 4 days, enhanced computed tomography showed superior mesenteric artery (SMA) thrombosis and intestinal necrosis. Therefore, emergency intestinal resection and PD catheter removal were performed, and then antithrombosis therapy was initiated. Because the patient’s abdominal pain was improved and platelet count and d-dimer concentration were reduced by these treatments, he was discharged from the hospital after 47 days. Thus, we report a rare case of culture-negative PD-associated peritonitis, which was caused by SMA thrombosis and intestinal necrosis. It is likely that combination of severe calcification of SMA and prolonged thrombocytosis secondary to the severe anemia contributed to the thrombosis.