Objective: To evaluate the incidence of consecutive exotropia following bilateral medial rectus muscle recession surgery (BMR) for esotropia using non-absorbable compared with absorbable sutures in children undergoing strabismus surgery. Methods: A retrospective cohort study of all children with esotropia who underwent BMR by a single surgeon in a tertiary public hospital. As of February 2018, only non-absorbable sutures were used. The primary outcome was the incidence of consecutive exotropia. Results: A total of 121 children were included in the analysis, 3.66 ± 2.62 years, 53% were male. In 80 children (66%) non-absorbable sutures were used (non-absorbable group) and in 41 children (34%) absorbable sutures were used (absorbable group). Consecutive exotropia (≥ 8 prism dioptres) occurred in ten children (24%) in the absorbable group and in three children (4%) in the non-absorbable group (OR = 8.28, 95% CI = 2.13–32.13; P = 0.002). This difference between groups remained significant after adjustment for potential confounders and follow-up time (HR = 4.98, 95% CI = 1.30–19.05, P = 0.019). Mean follow-up time was 22 and 12 months in the absorbable and non-absorbable groups, respectively (P < 0.001). Two children in the non-absorbable group had pyogenic granuloma that resolved after 3 months of topical steroidal therapy. Conclusion: Routine use of non-absorbable sutures in BMR surgery for esotropia may be a preferable alternative to absorbable sutures for the prevention of consecutive exotropia.