Background Sacrococcygeal pilonidal sinus is a common disease in young adults with male predominance causing significant morbidity. There is no ideal method for the management of pilonidal sinus. Limberg flap is a technique for managing pilonidal sinus that provides eradication of the sinus and tension-free wound closure; however, the lower end of the wound is found at the midline near the anus getting liable for maceration, infection, and acts as an entry for loose hair predisposing recurrence risk. Patients and methods In all, 92 patients with primary pilonidal sinus disease were subdivided into two groups. Group 1 patients were managed by the classic Limberg flap, while, group 2 patients were managed by a modified Limberg flap. Results Group 1 included 46 patients with a mean age of 25.48±5.403 years and 46 patients in group 2 with a mean age of 24.15±4.789 years. The disease duration was 14.2174±5.8686 months in group 1 versus 15.6739± 5.812 months in group 2; P values were 0.216 and 0.235, respectively. Wound maceration was higher in group 1 than in group 2, P value of 0.014. There was disease recurrence in two patients in group 1 while there was no recurrence in group 2 (P=0.495). Conclusion The modified rhomboid flap technique is a good option for the management of pilonidal sinus disease. It shifts the lower end of the wound away from the midline that decreases wound maceration and may decrease the possibility of disease recurrence.