Purpose: This study aimed to evaluate long-term outcomes after anal fistula surgery from university hospitals in Thailand. Methods: A prospectively collected database of patients with cryptoglandular anal fistula undergoing surgery from 2011 to 2017 in 2 university hospitals was reviewed. Outcomes were treatment failure (persistent or recurrent fistula), fecal continence status, and chronic postsurgical pain. Results: This study included 247 patients; 178 (72.1%) with new anal fistula and 69 (27.9%) with recurrent fistula. One hundred twenty-one patients (49.0%) had complex fistula; 53 semi-horseshoe (21.5%), 41 high transsphincteric (16.6%), 24 horseshoe (9.7%), and 3 suprasphincteric (1.2%). Ligation of intersphincteric fistula tract (LIFT) was the most common operation performed (n=88, 35.6%) followed by fistulotomy (n=79, 32.0%). With a median follow-up of 23 months (interquartile range, 12–45 months), there were 18 persistent fistulas (7.3%) and 33 recurrent fistulae (13.4%)—accounting for 20.6% overall failure. All recurrence occurred within 24 months postoperatively. Complex fistula was the only significant predictor for recurrent fistula with a hazard ratio of 4.81 (95% confidence interval, 1.82–12.71). There was no significant difference in healing rates of complex fistulas among seton staged fistulotomy (85.0%), endorectal advancement flap (72.7%), and LIFT (65.9%) (P=0.239). Four patients (1.6%) experienced chronic postsurgical pain. Seventeen patients (6.9%) reported worse fecal continence. Conclusion Overall failure for anal fistula surgery was 20.6%. Complex fistula was the only predictor for recurrent fistula. At least 2-year period of follow-up is suggested for detecting recurrent diseases and assessing patient-reported outcomes such as chronic pain and continence status.