Abstract Background Fistula in ano is a very common perianal condition seen in outpatient departments. Fistulotomy and fistulectomy are two conventional options of surgery. The present study is designed to observe wound healing time and mean postoperative pain score in the comparison of outcome of the fistulectomy to fistulotomy with marsupialization. Methods This prospective randomized trial was conducted in the surgical department of the Civil Hospital Karachi for a period of 12 months, in which 60 patients with low anal fistula were divided into 2 groups. Thirty patients in group A were treated with fistulectomy, and 30 in group B were treated with fistulotomy with marsupialization. The postoperative pain severity was assessed after 24 hrs through a visual analogue scale and on weekly and fortnightly follow-ups for 6 weeks. Wound healing was assessed by clinical examination on weekly and fortnightly follow-ups for 6 weeks to estimate the mean healing time. Results The mean pain score was significantly lower in group B in comparison to group A (3.6±1.99 versus 2.40±1.52; p=0.01). The mean wound healing time was shorter in group B in comparison to group A (4.23±0.77 versus 5.80±0.41 weeks; p=0.0005). Conclusion Fistulotomy with marsupialization is a simple, easy, and more effective method than fistulectomy for the treatment of simple perianal fistula.