Patients with perianal fistulas are frequently treated by a knotted seton which is well-known for causing complaints. We aimed to assess the feasibility of the knotless SuperSeton and advantages with respect to perianal disease activity. In a prospective cohort study, we included all consecutive adult patients with a knotted seton in situ or a perianal fistula requiring new seton drainage. Primary endpoint was seton feasibility (maintenance of the connection for minimally three months). Secondary endpoints included improvement of the Perianal Disease Activity Index (PDAI), complications and re-interventions within three months of follow-up. PDAI scores of patients with a knotted seton were crossover compared to PDAI scores after knotless seton replacement. Sixty patients (42% male, mean age 42 (SD 13.15), 41 with Crohn’s disease) were included between August 2016 and April 2018. Of 79 knotless setons, 69 (87.3%) stayed connected for ≥ 3 months. Overall, the knotless seton significantly decreased discharge (P = 0.001), pain (P < 0.001) and induration (P < 0.001) measured by the PDAI when compared to baseline. In patients with a knotted seton, replacement by the knotless seton significantly decreased discharge (P = 0.005) and pain (P < 0.001) measured by the PDAI. Furthermore, 71% of patients reported fewer cleaning problems compared to the knotted seton. Ten patients developed a perianal abscess, and five patients required a re-intervention. This study supports the feasibility of the knotless seton with promising short-term results. The knotless seton might be preferred over the knotted seton in terms of perianal disease activity.