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Background and objective: The gold standard for the treatment of chronic anal fissure is lateral internal sphincterotomy. Botulinum toxin injection provides temporary alleviation of sphincter spasm and allows the fissure to heal. This study aimed to compare the outcomes of lateral internal sphincterotomy and botulinum toxin injection treatments in patients with uncomplicated chronic anal fissure. Methods: A prospective comparative study was carried out at the surgical unit of Erbil teaching hospital, Erbil, Kurdistan Region of Iraq, from January 2017 to February 2018. Fifty-five patients were enrolled in this study. Five patients were excluded, and the remaining 50 patients were equally divided into two groups. Group A was managed with lateral internal sphincterotomy and group B with botulinum toxin. Postoperative pain relief, bleeding, fissure healing, incontinence, and relapse after six weeks and three months of follow-up were compared. Results: One month after treatment, 12% of the lateral internal sphincterotomy group had bleeding, while none of the botulinum toxin group (P = 0.234). Two patients (8%) of the lateral internal sphincterotomy group had pain while one (4%) of the botulinum toxin group (P >0.999).Three months after treatment, 4% of the lateral internal sphincterotomy group had bleeding, while none of the botulinum toxin group (P >0.999). None of the lateral internal sphincterotomy group had pain while one (4%) of the botulinum toxin group (P >0.999). Regarding healing, 96% of the lateral internal sphincterotomy group healed, while 92% in the botulinum toxin group (P >0.999). Conclusion: The outcome of lateral internal sphincterotomy and botulinum toxin were nearly the same, but lateral internal sphincterotomy required hospitalization, period off work, and risk of anesthesia. These risks were absent in botulinum toxin injection.