OBJECTIVE: This study aims to present a unique case of acanthamoeba keratitis (AK) with a delayed diagnosis and prolonged usage of glucocorticoid eye drops. Subsequently, the patient developed cytomegalovirus corneal endotheliitis (CMVCE), leading to severe ocular complications. To the best of our knowledge, this is the first documented case of confirmed CMVCE subsequent to AK. METHODS: A 32-year-old male patient with a history of contact lens usage and extended administration of glucocorticoid eye drops for keratitis underwent deep anterior lamellar keratoplasty (DALK) in the left eye. The diagnosis of AK was delayed by 4 months. Following corneal endothelial decompensation, penetrating keratoplasty (PKP) was performed 5-month post-DALK. Intraoperatively, the presence of CMV in aqueous humor and corneal tissue was confirmed using multiplex qPCR, validating the diagnosis of CMVCE. Despite aggressive antiviral therapy, the patient's left-eye condition continued to worsen, leading to a combined phacoemulsification and trabeculectomy in the left eye, as well as supplementary Ahmed valve drainage. RESULTS: Following four surgical procedures and subsequent follow-up, the patient's left-corneal graft remained clear, intraocular pressure was well-regulated, the eye was preserved, and some degree of vision was retained. CONCLUSION: CMVCE subsequent to AK represents a severe form of infectious corneal keratopathy. In AK patients experiencing unexplained corneal endothelial decompensation, mydriasis, iris atrophy, concurrent cataract, and secondary glaucoma post-keratoplasty, a reoccurrence of AK should not be considered in isolation. CMV infection should also be suspected, and an aqueous humor test should be conducted to confirm the diagnosis.