Comamonas species are rarely associated with human infections. Recent reports found that Comamonas kerstersii was associated with severe diseases such as abdominal infection and bacteremia. However, Comamonas kerstersii may be confused with Comamonas testosteroni using the automatic bacterial identification systems currently available. An 8-year-old boy who had a right iliac fossa pain and classic migration of pain at the temperature of 38.9°C. The positive strain of aerobic and anaerobic bottles of blood cultures was identified. The patient was diagnosed as acute peritonitis and perforated appendix with abdominal abscess. The bacterium was identified by routine methods, MALDI-TOF-MS. The patient was treated with exploratory laparotomy, appendectomy, tube drainage, and prescribing antibiotic treatment. The patient was discharged with complete recovery. The organisms were confirmed as Comamonas kerstersii by MALDI-TOFMS and a combination of the other results. Our findings suggest that Comamonas kerstersii infection occurs most often in association with perforated appendix and bacteremia. We presume that Comamonas kerstersii is an opportunistic pathogen or commensal with the digestive tract and appendix bacteria.