In the treatment of chronic anal fissure, both surgical and topical treatment methods are used. The purpose of this study was to research a combined topical treatment that we prepared and to compare the effectiveness of lateral internal sphincterotomy in chronic anal fissure with this topical treatment. A total of 183 patients with chronic anal fissure were divided into two groups. One hundred and four patients had topical medical treatment (group 1) and seventy-nine patients underwent lateral internal sphincterotomy (group 2). In the first group, a topical combination of ointments consisting of bacitracin-neomycin sulfate, dexpanthenol, and diltiazem was applied to the anal area. Four weeks after treatment, pain and bleeding during defecation, gas/fecal incontinence, treatment-related adverse events and recovery rates were evaluated in both groups. Also, patients were examined for recurrence between the 8th and 10th weeks. There was no significant difference in recovery rates between the groups. In group 1, recovery rate was 82.7%, while in Group 2 it was 92.4% (p = 0.054). In both groups, gas/fecal incontinence ratio was significantly different, supporting the medical treatment (p = 0.02). The severity of pain and bleeding during defecation were compared between the groups. Only the severe pain was significantly higher in the medical treatment group (p = 0.018). The recurrence rate was 5.8% in the medical treatment group, but no recurrence was detected in the surgical group. Due to possible complications of surgical treatment and similar recovery rates, medical treatment of patients with chronic anal fissure can be tried before surgical treatment.