Purpose: Crohn’s disease (CD) is mainly presenting gastrointestinal symptoms but also may involve perianal diseases, with anal fistula being the most common. Anal fistula surgery performed without recognition that the patient has CD increases the complications such as delayed wound healing and anal sphincter injury. This study aimed to investigate clinical symptoms and surgical findings that could allow early diagnosis of CD in patients aged 10 to 19 years who underwent anal fistula surgery. Methods: Among the 320 patients under the age of 19 who underwent anal fistula surgery, those who were diagnosed with tuberculosis fistula were excluded, medical records of 316 patients were examined. We investigated the characteristics of anal fistula and postoperative wounds as well as the colonoscopic and surgical findings. Results: Compared to 272 patients not diagnosed with CD (non-CD group), 44 patients diagnosed with CD (CD group) showed significantly higher levels of C-reactive protein as well as anal discharge, family history of inflammatory bowel disease, history of anal fistula, diarrhea, abdominal pain, weight loss, complex anal fistula, recurred anal fistula, delayed wound healing and friable/edematous/granulation of surgical site. Conclusion For patients aged 10–19 years with anal fistulas, emphasizing early suspicion and an active diagnostic work-up is essential for early diagnosis of CD.