Background – Anal fissure is a crack or split in the vertical axis of the Squamous lining of the anal canal. There are so many surgical and nonsurgical management to treat chronic anal fissure by reducing hypertonia of internal anal sphincter. In this study a surgical procedure lateral anal sphincterotomy is compared with a nonsurgical procedure injection of botulinum toxin into internal sphincter. Methods – This is a prospective comparative study conducted in Medical College Kolkata. Total 100 were randomized into two groups. One group of 50 patients randomly assigned for Lateral Anal Sphincterotomy another 50 patients underwent 20 IU Botulinum toxin injection into internal sphincter and two groups advised for follow up at 2 weeks, 6 weeks and 6 months. Results – 98% of botulinum toxin group satisfied regarding complete relieved of pain but 84 % in case of LS group after 6 months (p=0.036). After 6 months no patient complaints about incontinence in BT group but 16% in case of LS group (p=0.0360). 2% of BT group complains about recurrence but 15% cases came with recurrence in case LS group. Conclusion– Local infiltration of botulinum toxin into internal sphincter (single dose 20 IU) is as good as first line treatment option in cases of chronic anal fissure.