Glaucoma is one of the world’s leading causes of irreversible vision loss. It is often asymptomatic until it reaches an advanced stage, which can have a significant impact on patients’ daily lives. This paper describes the case of a 50-year-old female patient who presented with acute onset of ocular pain, photophobia, and loss of visual acuity in her right eye (RE). The patient’s medical history includes congenital cataracts, surgical aphakia, nystagmus, strabismus, amblyopia, and secondary glaucoma. Ophthalmological examination showed BCVA RE-hand movement, left eye (LE)—0.08 with an intraocular pressure (IOP) of 30 mmHg in RE and 16 mmHg in LE. Biomicroscopic examination of RE showed corneal graft, epithelial and endothelial edema, endothelial precipitates, corneal neovascularization, aphakia, and Ahmed valve superotemporally. Despite maximal topical and systemic treatment, Ahmed valve, and trabeculectomy, secondary glaucoma in the right eye remained refractory. Reimplantation of an Ahmed valve was performed. This resulted in a favorable outcome with increased visual acuity and controlled intraocular pressure. The combination of aphakia, penetrating keratoplasty, and secondary glaucoma is a challenge for any surgeon. It is important that both the perioperative risks and the possible complications are carefully assessed in each patient, especially if associated pathology is present.