©Copyright 2021 by Gazi University Medical Faculty - Available on-line at web site http://medicaljournal.gazi.edu.tr/Background: The principal objectives in the treatment of pilonidal sinus are to excised the sinus canal without recurrence, limit morbidity and hospital stay and have low cost. Although there are many reported articles in the literature, pilonidal sinus disease treatment in children is controversial currently. This study’s aim was to compare two surgical techniques which is used in the pilonidal sinuses treatment in terms of complications and recurrence. Methods: This study included 122 pediatric patients with sacrococcygeal pilonidal sinus who are operated by primary repair method (PRM), or Limberg flap method (LFM) on between January 2010 and January 2019. The surgical methods were analyzed and compared in terms of demographic datas, body-mass index, postoperative infection, postoperative bleeding, recurrence, treatment of recurrence, and time between operations. Results: Sixty two patients (50.8%) were treated with the PRM, and 60 patients (49.2%) were treated with the LFM. In the postoperative period of the PRM, 12 patients had wound infection, seven patients had bleeding and granulation, and eight patients had recurrence. In the LFM group, six patients had wound infection, three patients had bleeding and granulation, and two patients had recurrence. Postoperative complications were less in LFM group. (p = 0.026). Conclusion: Based on this study, we recommend the LFM because it has fewer complications and lower recurrence rates.