Background and Objectives: Patients with cataract and age-related macular degeneration (AMD) may safely undergo cataract phacoemulsification to enhance visual acuity. Although it has not been proven that cataract surgery can cause AMD progression, different phacoemulsification effects are observed not only on retinal but also on choroidal tissues. The purpose of this study was to evaluate the effect of phacoemulsification on the choroidal thickness (CT) in eyes with and without AMD. Materials and Methods: In 32 eyes of 32 patients with senile cataract (No-AMD group) and in 32 eyes of 32 patients with cataract and dry AMD (AMD group), who had phacoemulsification without intraoperative complications and intraocular lens implantation, foveal retinal thickness (FRT) and CT were evaluated three times: at 1–2 post meridiem preoperatively, then 1 month and 3 months postoperatively, using 1050 nm swept source-optical coherence tomography (Topcon, Tokyo, Japan). Results: In both groups, a significant increase in FRT was observed after one month and a decrease after three months without reaching the baseline. One month after surgery, a sectorial CT increase was apparent in all sectors in both groups. A negative association between CT and age was disclosed in the No-AMD group almost for all regions at all time points. Furthermore, CT was significantly negatively associated with axial length (AL) in all sectors at all time points in the AMD group. Conclusion: Uneventful phacoemulsification may induce changes in the posterior eye segment. An increase in CT and FRT was observed in both groups one month after the surgery. However, three months after surgery, CT changes were different in both groups, while FRT decreased in both groups. CT changes negatively associated with age in the No-AMD group and with AL in the AMD eyes. These postoperative changes in the choroid and retina may not only lead to the late-onset pseudophakic cystoid macular edema but also to progression of AMD.