Background: To assess the long-term outcomes of phacoemulsification and intraocular lens (IOL) implantation in eyes with uveitis. Methods: One hundred and five eyes of 81 patients, who underwent phacoemulsification and IOL implantation between January 2009 and July 2016, were included in this study. The demographic data, preoperative clinical findings, postoperative outcomes, and intraoperative and postoperative complications were recorded. All collected data and risk factors with regard to visual prognosis were analyzed with the help of the Statistical Package for the Social Sciences version 20.0 software program (IBM Corp., Armonk, NY, USA). Results: During follow-up (mean: 35.2 ± 22.2 months), corrected distance visual acuity (CDVA) improved in 87.7% of all eyes and reached a level of 0.3 LogMAR or greater in 61.3% of eyes. Postoperative complications included posterior capsule opacification (50.9%), posterior synechiae (21.7%), cystoid macular edema (16%), epiretinal membrane (13.2%), glaucoma (11.3%), increased intraocular pressure (8.5%), and severe inflammation (6.6%). Uveitis recurred in 55.7% of all eyes. The risk for the development of cystoid macular edema was found to be associated with recurrence in the early postoperative period. Low visual acuity risk was 11.1-fold higher with macular scarring (p = 0.001) and 14-fold higher with optic atrophy (p < 0.001), respectively. Conclusions: With appropriate management during the pre-and postoperative periods, phacoemulsification and IOL implantation surgery can be safe and effective in eyes with uveitis. However, great caution must be taken to prevent complications both before and after the surgery.