Purpose: To investigate the effects of horizontal and oblique strabismus surgery on the corneal endothelial cell layer. Methods: Eighty-three eyes of 56 patients were prospectively evaluated. Corneal endothelial cell layer analysis was performed with a specular microscopy device (EM-3000; Tomey Corporation) preoperatively and 1 day, 2 weeks, and 2 months postoperatively. Endothelial cell density, coefficient of variation, average cell area, standard deviation (SD) of the endothelial cell area, hexagonality, and central corneal thickness (CCT) were evaluated. Results: Endothelial cell density, average cell area, and SD of the endothelial cell area did not show a statistically significant change postoperatively. In the one and two horizontal muscle surgery groups, the hexagonality measurements 2 weeks postoperatively were significantly lower compared to preoperative values. In the one horizontal muscle surgery group and when all patients were examined, CCT 1 day postoperatively was significantly higher than 2 weeks postoperatively. No significant change was observed postoperatively in any of the endothelial parameters in the oblique surgery group. Spherical equivalent was positively correlated with endothelial cell density and CCT, and it was negatively correlated with the average cell area and age. Age was positively correlated with the average cell area and the SD of the endothelial cell area, negatively correlated with endothelial cell density and hexagonality, and was not correlated with the coefficient of variation or CCT. Conclusions: There is a temporary effect of horizontal strabismus surgery on hexagonality and corneal thickness. A definite decrease in cellular hexagonality occurs as the number of endothelial cells decrease and cell areas increase with age. [ J Pediatr Ophthalmol Strabimus . 2021;58(4):254–260.]