Rationale  There is a need for a low cost treatment for complex anal fistulas that can heal without causing fecal incontinence, with room for the study of herbal medicines. Objective  To evaluate the effect of the glycerin Aloe barbadensis Miller extract in the treatment of anal fistula in rats. Method  Thirty Wistar rats underwent peritoneal anesthesia with ketamine and Xylasine, followed by transfixation of the anal sphincter with a steel wire, which remained for 30 days to develop the anal fistula. After this period, the steel wire was removed and three groups with 10 animals were formed: A (control), without treatment; B (seton), in which a cotton seton was introduced; C (therapeutic seton), in which a cotton thread was introduced as a seton, and Aloe barbadensis Miller extract was daily dripped in the seton; after 30 days, the setons of groups B and C were removed, and after two weeks without a seton euthanasia and removal of specimens was conducted, and the fistula closure and the inflammatory process were analyzed. Results  Fistula persistence was observed in all animals in Group A, six in Group B and three in Group C ( p  = 0.015). The mean local inflammation levels were 0.9 in Group A; 0.8 in Group B, and 0 in Group C ( p  = 0.015). Conclusion  The use of a seton soaked in a glycerin Aloe barbadensis Miller extract was effective in the healing of anal fistulas in rats, in addition to causing less inflammatory process than the non-phytotherapeutic seton.