There are few studies comparing methods for pilonidal cyst closure. This study was conducted to compare simple surgical closure, secondary healing, and closure using a Limberg flap in the treatment of patients affected with pilonidal cysts. In total, 150 patients with pilonidal cysts were selected and randomized into 3 groups, with 50 participants in each group. Group A underwent primary closure, Group B underwent secondary closure, and Group C underwent closure with a Limberg flap. Operating time, amount of pain after surgery, time to mobilization, time until return to work, time for complete healing, time until being able to sit on the toilet without pain, postoperative complications including infection and recurrence, and seroma and edema after surgery were compared among the 3 groups. Duration of surgery in the Limberg flap group was significantly longer than the duration of surgery in Group A or Group B (p < .001). The time to patient mobilization, the time when the patient returned to work, the time to complete healing, and the time to being able to sit on the toilet without pain were significantly shorter in Group C than in Group A or Group B (p < .001). Although the procedure takes longer when using a Limberg flap, it appears to be a more effective method in the surgical treatment of patients with pilonidal cyst because of the reduced healing time and improved functional status after the procedure.