Background Various surgical procedures are available for the treatment of pilonidal sinus diseases (PSD), but the best surgical approach remains controversial. Minimally invasive surgical procedures are more popular than surgery. This study aimed to evaluate the efficacy of sinusectomy with primary closure (SPC) in comparison with excision and primary closure (EPC) in primary or recurrent cases. Materials and methods This single-center retrospective cohort study was conducted with two cohort groups in which 351 patients with PSD underwent either SPC or EPC. The two procedures were compared according to the presence of short-term complications and recurrence of PSD. Results Of the patients, 134 underwent EPC and 217 underwent SPC. The length of stay and the wound healing time were significantly longer in the EPC group than in the SPC group. The occurrence rates of wound site infection and abscess were significantly higher in the EPC group than in the SPC group; however, seroma was statistically significantly more common in the SPC group than in the EPC group. The recurrence rates were 18.7% and 5.5% in the EPC and SPC groups, respectively. Conclusion SPC is an efficient procedure for the treatment of patients with PSD showing simple and complicated disease patterns.