Purpose: To evaluate the immediate alterations in the thickness of the macular ganglion cell–inner plexiform layer (mGCIPL), peripapillary retinal nerve fiber layer (RNFL), inner retinal layer (IRL), and outer retinal layer (ORL) using spectral domain optical coherence tomography (SD-OCT) subsequent to strabismus surgery in pediatric patients diagnosed with horizontal esotropia. Methods: Twenty-eight eyes from twenty-one child patients who had undergone uncomplicated horizontal rectus muscle surgery due to strabismus were included. Measurements of RNFL, mGCL-IPL, IRL, and ORL using structural OCT were conducted both before the surgery and one month after the surgical procedure. Importantly, a control group comprising 14 healthy eyes, matched for age and significant refractive error (p = 0.026). Notably, comparison between the strabismus group at baseline and the healthy group revealed a significant reduction in mGCL-IPL in the strabismus group (60.8 ± 9.2) compared to the healthy control group (68.3 ± 7.2; p = 0.014). Conclusions: Following strabismus surgery, our observations pointed towards a thickening of the mGCL-IPL layer, which is likely attributable to transient local inflammation. Additionally, we identified a significant differentiation in the mGCL-IPL complex between the pediatric patient group with strabismus and the control group.