•Rare fungus causes endophthalmitis leading to enucleation.•Misdiagnosis and treatment of uveitis with prednisone before a definitive diagnosis.•Significance of proper clinical management of a suspected fungal infection.•Causative organism is Paradictyoarthrinium diffractum. During outdoor work in April 2022, a 48-year-old man was stabbed by a tree branch and underwent intraocular foreign body extraction and repair of the scleral wound with sutures and amniotic membrane graft at a local hospital. Steroid therapy with prednisone was prescribed after a diagnosis of uveitis. Vitrectomy was performed in June 2023; a fungal culture was positive, and ITS sequencing identified the organism as Paradictyoarthrinium diffractum. Empiric antifungal therapy did not have an effect, and, because of deterioration of the condition, the left eye was enucleated in October 2023. P. diffractum is a mangrove host-specific saprophytic fungus that has not been reported in humans.