To investigate the effect of the most commonly performed strabismus surgery procedures on the blood-aqueous barrier using laser flare photometry (LFP). Patients who underwent unilateral or bilateral strabismus surgery between January 2020 and May 2021 were included. Eyes were grouped according to the number of rectus muscles operated: one rectus muscle procedure (recession) with or without inferior oblique anterization (IOA), ipsilateral two rectus muscle procedure (recession and resection) with or without IOA, and unoperated fellow eyes of patients undergoing unilateral surgery. Anterior chamber flare values were measured by LFP for each eye the day before the surgery and day 1, week 1, and month 1 postoperatively. A total of 66 eyes of 33 patients (21 females) were included. There were 29 eyes in the one-muscle group, 22 in the two-muscle group, and 15 in the fellow-eye group. The mean flare values of the two-muscle group were significantly higher than those of the other groups at postoperative day 1 and week 1 (P = 0.001, for both). The mean postoperative day 1, week 1, and month 1 flare values of the two-muscle group were significantly higher than the mean preoperative flare value. There were no significant differences between pre- and postoperative flare values of the one-muscle or fellow-eye groups (P > 0.05, for both). In our study cohort, LFP provided evidence of subclinical changes in the blood-aqueous barrier up to the first month postoperatively in otherwise healthy patients undergoing two-muscle surgery compared with those undergoing one-muscle surgery and unoperated fellow eyes.