Most patients with acute appendicitis have typical symptoms and physical examination findings, yet some patients may have an atypical clinical presentation that is indistinguishable from other alternative conditions that are included in the differential diagnosis. The clinical role of colonoscopy for the diagnosis of acute appendicitis in these patients has not been investigated. Here, we describe the case of a 44-year-old man with acute appendicitis that was diagnosed with colonoscopy, which was performed 8 days after the development of abdominal pain, and colonoscopy demonstrated the frank pus drainage from the appendiceal orifice. An emergency laparoscopic partial cecectomy with an appendectomy was performed based on the colonoscopy findings. The microscopic findings were consistent with an acute suppurative appendicitis with periappendiceal adhesions, dense fibrosis and inflamed granulation tissue. This case highlights that timely colonoscopy may be helpful for the confirmation or exclusion of appendicitis when the clinical presentation is atypical.