To evaluate the changes in retrobulbar circulation after strabismus surgery and to assess the relationship of these changes with choroidal thickness (CT). This prospective study included 26 eyes of 26 patients who underwent strabismus surgery and 15 eyes of 15 healthy individuals as control group. The patients who had single horizontal muscle surgery were included in Group 1 (n = 14); and those who had surgery on both horizontal muscles were included in Group 2 (n = 12). Peak systolic velocity (PSV), end-diastolic velocity (EDV), resistive index (RI) and pulsatility index (PI) of ophthalmic artery (OA), posterior ciliary artery (PCA), and central retinal artery (CRA) were measured using Color Doppler Ultrasonography. Subfoveal CT was measured via Optical Coherence Tomography. All measurements were obtained preoperatively, at 1st week and 1st month after surgery. There were no differences regarding preoperative blood flow velocity parameters among the groups. OA RI increased significantly at 1st week and 1st month after surgery in Group 1 and 2 (P = 0.029 and P = 0.045, respectively). There was a significant increase in PCA PSV at 1st week in Group 1 (P = 0.002). There was no difference between the mean preoperative and postoperative CT among the 3 groups. A negative correlation between the percentage changes of CT and CRA EDV was found in Group 2 (P = 0.011). Single and double horizontal rectus muscle surgery have a measurable effect on retrobulbar hemodynamics but these changes do not correlate with CT.