Background: There is no consensus on the optimal dosage of botulinum toxin (BT) as a sphincter sparing alternative to lateral internal sphincterotomy for chronic anal fissure. The aim of this study was to assess the long-term efficacy of high-dose BT as well as the presence of incontinence following the treatment of chronic anal fissure at a single institution. Methods: A retrospective case–control study was performed at a single institution over a 6-year period (2009–2014). Patients given high-dose (80–100 IU) BT were compared to low-dose (20–40 IU) case controls. Clinical notes were reviewed, and follow-up was carried out via a telephone questionnaire. Results: One hundred and fifty-eight patients were treated with BT injections within the study period (103 high dose; 55 low dose). The mean length of follow-up was 25 months (range 4–52 months). Classic posterior fissures with high anal tone were more prevalent in the low-dose group (40 vs 47%, p = 0.3). Patient satisfaction was higher in the high-dose group (90 vs 78%, p = 0.05). Long-term recurrence (6 months after the last treatment) was also lower (23 vs 53%, p = 0.0001) on multivariate analysis. No long-term incontinence was observed. Conclusions: In this series, the recurrence rate post-BT injection was significantly lower in the high-dose group. There was no long-term incontinence. Further studies are needed to confirm our results.