BackgroundPrior studies focus primarily on surgical outcomes of anal fistula treatment, such as healing rates, rather than patient‐reported outcomes, such as postoperative pain, which could influence surgical choice.ObjectiveTo compare pain scores at 6 and 24 h postoperatively between laser closure and ligation of the intersphincteric tract for anal fistula.DesignProspective, double‐blinded randomized controlled trial.SettingsA quaternary hospital in Malaysia.PatientsPatients aged 18–75 years with high transsphincteric fistulas.InterventionFistula laser closure versus ligation of the fistula tract (LIFT) treatment.Main Outcome MeasuresPain scores, continence, quality of life (QOL), operative time, and treatment failure were compared using chi‐square, Fisher's exact test, student t‐test, or Mann–Whitney with p < 0.05 denoting statistical significance.ResultsFifty‐six patients were recruited (laser, n = 28, LIFT, n = 28). Median pain scores for laser versus LIFT at 6 h postoperatively were 1.0 versus 2.0 (Rest, p = 0.213) and 3.0 versus 4.0 (Movement, p = 0.448), respectively. At 24 h, this reduced to 2.5 in both arms at rest (p = 0.842) but increased to 4.8 versus 3.5 on movement (p = 0.383). Median operative time for laser was significantly shorter (32.5 min) than LIFT (p < 0.001). Laser treated patients trended toward quicker return to work (10.5 vs. 14.0, p = 0.181) but treatment failure was similar (54% vs. 50%, p = 0.71). No patients developed postoperative incontinence. Mean SF‐36 scores increased from baseline (67.1 ± 17.0; 95% CI 63.6–82.4 vs. 71.3 ± 11.4; 95% CI 64.0–75.0) to 6 months postoperatively (77.7 ± 21.0; 95% CI 57.0–80.3 vs. 74.0 ± 14.3; 95% CI 67.6–81.4) regardless of the type of surgery (P > 0.05).LimitationsPatients with prior fistula surgery (approximately 20%) led to heterogeneity. The total laser energy delivered varied depending on fistula anatomy.ConclusionLaser fistula closure is an alternative to LIFT, with similar postoperative pain and shorter operative time despite more complex fistula anatomy in the laser arm, with a greater improvement in QOL.Trial RegistrationClinicalTrials.gov: NCT06212739.