Pilonidal sinus (PS) disease is a chronic inflammatory disease of the sacrococcygeal region. Although various methods have been described for surgical treatment, there is no consensus on the best surgical technique. The aim of this study was to present the results of a new advancement flap technique named the “Keystone flap (KSF)” and compared with the Limberg flap (LF) technique in pilonidal sinus surgery. A retrospective review was made of 124 consecutive patients surgically treated for PS disease with KSF and LF procedures. Baseline characteristics, operation time, volume of excised specimen, duration of hospitalization, duration of drainage, duration of healing, time to return to work, local complications and recurrence were evaluated and compared between the two procedures. Operation time, healing time, and time to return to work were significantly shorter in the KSF group. Partial wound dehiscense and prolonged wound healing were more common in the LF group. An additional intervention in the operating room was required by 21.1% of the LF group and was a significantly lower rate in the KSF group at 7.5%. There was no significant difference between the groups in terms of recurrence. The KSF procedure seems promising for treating pilonidal sinus disease, with the advantages of shorter operation, healing, and return to work times. It also provides lower partial wound dehiscence and necrosis rates.