A pilonidal abscess is an emergency situation which requires immediate drainage and is usually seen in young men. We aimed to compare incision and draining (I&D) of acute pilonidal abscess (PSA) and healing by secondary intention with I&D and subsequent delayed pits excision and closure (PE/PC). A total of 62 patients admitted with PSA were randomized to undergo either I&D and healing by secondary intention (group 1, n = 33) or I&D and PE/PC (group 2, n = 29). Demographic characteristics of the patients, abscess depth and location, duration and healing times of the symptoms, time required to return to work, and ratio of chronic pilonidal sinus (PNS) development were recorded, and the two methods were compared. No statistically significant differences were found between the groups in relation to sex, age, and preoperative findings, including discharge, infection, pain, and length and depth of abscess. There was no difference in length of hospital stay between the groups, and no statistically significant difference was found between the groups in terms of complication rate (P = 0.298). A statistically significant difference (P = 0.033) was, however, found between the two groups in the recurrence rate of a pilonidal abscess (9.09% in group 1 versus 3.44% in group 2). A statistically significant difference was also observed between the groups in terms of development of chronic PNS (P = 0.020). According to the results of our study, I&D and PE/PC should be the primary procedure used, as opposed to skin incision, curettage, and secondary healing for the treatment of PSA.