Purpose: Pilonidal sinus disease is a common condition, which mostly affects young men. While various surgical techniques have been introduced for treating intergluteal pilonidal disease (IPD), controversies still exist regarding the best surgical approach. The purpose of this study was to compare the efficiency and the short-term outcomes of Limberg flap and Karydakis flap surgeries for the treatments of patients with IPD. Methods: A total of 80 patients with IPD who had underwent either Karydakis flap (KF group: n = 37) or Limberg flap (LF group: n = 27) surgery between January 2015 and January 2016 at Imam Khomeini Hospital of Sari in the North of Iran were recruited for inclusion in this randomized, single-blind study. Results: Compared to the KF group, the LF group showed faster complete wound healing, longer duration of surgery and hospital stay, larger wound size, and shorter period of incapacity for work. The overall patient satisfaction in the LF group was significantly higher than that in the KF group. The visual analogue scale score of pain was lower in the LF group than in the KF group. Also, the overall frequency of postoperative complications was higher in the KF group than in the LF group. Recurrence was reported in one patient from the KF group. Conclusion: Given the lower rate of postoperative complications and greater cosmetic satisfaction of patients, the Limberg flap procedure should be selected, instead of the Karydakis flap procedure, as the standard technique for treating patients with IPD.