The most appropriate surgical treatment for pilonidal sinus disease (PSD) is still in dispute. This study aims to comprehensively compare the outcomes of surgical interventions using network meta-analysis. Randomized controlled trial studies were searched systematically to identify all eligible studies in multiple databases and previous publications and Bayesian network meta-analysis was performed. Our primary outcome was the recurrence rate. Differences in the findings of the studies were explored in meta regressions and sensitivity analyses. The risk of bias of each study was assessed using the Cochrane risk of bias tool. Confidence in evidence was assessed using CINeMA (Confidence in Network Meta-Analysis). A total of 39 studies and 5,061 patients were identified and the most common surgical intervention was the Limberg flap. In network meta-analysis, modified Limberg flap and off-midline closure were associated with the lowest recurrence rate. However, the Karydakis flap was associated with shorter operation time by several minutes compared with other interventions and few significant results were found in other outcomes. Modified Limberg flap and off-midline closure provided relatively low recurrence and complications rates. Therefore, they could be two promising surgical interventions for PSD patients.