Background: pilonidal sinus (PNS) is a common condition. Although many methods for treatment are available, there is no consensus on the optimal treatment. Aim of the study: The aim of the work was to compare the outcome of sinotomy procedure with or without marsupialization versus sinectomy and primary closure with or without drain in the management of pilonidal sinus as regards operative times, postoperative complications, and time of healing and return of work. Patients and Methods: This is a comparative randomized comparative study.  Sixteen patients undergoing surgery for primary PNS were enrolled. The patients were randomized into four groups. Each group included 15 patients. Group A underwent sinotomy without marsupialization; group B underwent sinotomy with marsupialization; group C underwent limited excision and primary closure with a drain and group D underwent the same procedure as group C but without drain. Each patient was followed up for 6 months. Results: Significantly short operative time was recorded in group B. Postoperative wound complications occurred in 3.2% of patients in group A, in 1.7% of patients in B, in 7.4% of patients in group C and in 4.2% of patients in group D. Recurrence rate was a slightly higher in group C but with no statistical significance. Conclusion: The sinotomy with marsupialization for treatment of PNS is superior to excision with primary closure either with or without a drain and sinotomy without marsupialization.