Abstract Background and aim This study aims to evaluate the effect of time to Crohn’s disease (CD) diagnosis on perianal fistula (PAF) outcomes in patients with a fistula as first manifesting sign. Methods In this multicenter, retrospective study, CD patients with a PAF preceding CD diagnosis between November 2015 and June 2022 were included. The primary outcome parameter was the time to CD diagnosis and its correlation with long-term outcomes. Results In total, 126 patients with a PAF prior to CD diagnosis were identified. Median time to CD diagnosis was 15.0 months (IQR 3.8-47.3). A total of 49 patients (38.9%) had a clinically closed fistula of which 21 patients (42.9%) achieved radiological healing. 25 patients (19.8%) underwent defunctioning, of which 9 patients (36.0%) needed proctectomy. Median time to CD diagnosis was shortest in patients with radiological healing (4.0 months, IQR 2.0-16.5) or clinical closure without radiological healing (11.0 months, IQR 3.0-47.8). In patients without fistula closure (n=51), median time to CD diagnosis was significantly longer compared to patients with fistula closure, 18.0 months vs 8.0 months (p=0.031). In patients who needed defunctioning, median time to diagnosis was more than twice as long compared to patients without defunctioning, 30.0 months vs 12.0 months (p=0.054). Conclusion A prolonged time to CD diagnosis in patients with a PAF as a manifesting sign is associated with worse long-term outcomes. Patients in whom radiological healing could be achieved had the shortest time to CD diagnosis, emphasizing the relevance of increased clinical awareness of underlying CD in fistula patients.