We report a case of endophthalmitis occurring secondary to a retained cilium in a clear corneal wound after cataract surgery. A 67-year-old female presented to an ophthalmology emergency room with light perception vision in the right eye 5 days after routine cataract surgery. Examination of the right eye demonstrated decreased vision, conjunctival injection, a corneal endoplaque, and anterior chamber fibrin. Additionally, a cilium was visible in the clear corneal incision. A vitreous aspiration and injection of antibiotics and steroid were performed, and the patient underwent a vitrectomy the next day. Intraoperative cultures and culture of the cilium grew Staphylococcus epidermidis. One year after vitrectomy, the patient's vision recovered to 20/25 in the operated eye. In conclusion, a retained cilium in a clear corneal wound related to cataract surgery, though rare, may result in endophthalmitis. The surgical field should be cleared of cilia on the ocular surface prior to surgery. Proper draping and use of povidone-iodine antisepsis are essential in reducing the risk of endophthalmitis.