The best surgical technique for pilonidal sinus disease (PSD) is still disputed. The objective of this prospective randomized study is to compare the short and long-term results of modified Limberg flap and Karydakis flap surgeries that have been widely used in recent years. Ninety one patients were included in the study. The patients were divided into two groups: modified Limberg flap (MLF; n = 46) and Karydakis flap (KF; n = 45). Preoperative findings of the patients, their surgical findings, and short and long-term postoperative findings were recorded and statistically compared. While no significant difference was discovered between the groups in terms of postoperative analgesic need, hospital stay, postoperative infection rate, drain stay time, painless sitting time, painless toilet-sitting time, and painless walking time, return to work or school time was shorter in the MLF group compared with the KF group (20.61 +/- 7.89 days, 23.29 +/- 6.42, respectively; P < 0.05). Cosmetically, the visual analog scale (VAS) of the KF group was significantly higher than that of the MLF group (VAS score 7.12 +/- 1.28, 5.45 +/- 1.77, respectively; P < 0.05). Considering recurrence rates, no statistically significant difference was found between the groups. Our study found out that short and long-term results of the MLF and KF procedures are similar. We believe both methods can be safely used in surgical PSD treatment given that in the MLF procedure, shorter return-to-work time is achieved, while the procedure provides better cosmetic results.