Background and objective: No current nationwide consensus exists on pilonidal disease (PD) treatment in Switzerland and Austria. The objective of this study was to assess and compare the spectrum of PD treatment strategies in Switzerland and Austria. Materials and Methods: A survey including 196 certified institutions (Switzerland, N = 99 and Austria, N = 97) was performed. Treatment strategies for both chronic and acute pilonidal disease were investigated, as well as evolution of treatment over the last 20 years. Results: In total, 92 of 196 (47%) hospitals participated in the survey. Recurrence rate (20%) was similar between the two countries. In acute pilonidal disease, a two-stage approach with incision and drainage as the first step was preferred over a one-stage procedure in both countries. In Austria, all patients with chronic pilonidal disease were treated as inpatients, whereas 28% of patients in Switzerland were treated on an outpatient basis (p = 0.0019). Median length of hospital stay was double in Austria (four days) compared to Switzerland (two days; p < 0.001). Primary resection and off-midline closure (p = 0.017) and the use of tissue flaps (p = 0.023) were performed more commonly in Austria than in Switzerland. Minimally invasive techniques were performed more often in Switzerland than in Austria (52% vs. 4%, p < 0.001). Overall, wide excision with secondary wound healing or midline closures declined over the last 20 years. Conclusion: Treatment strategies for chronic PD differ between Austria and Switzerland with more and longer inpatient care in Austria, increasingly minimally invasive approaches in Switzerland, and outdated procedures still being performed in both countries. Overall, heterogeneity of practice dominates in both countries.