To describe a case of delayed-onset Aspergillus fumigatus endophthalmitis secondary to infectious fungal scleritis diagnosed with broad range polymerase chain reaction (PCR) from scleral nodular debridement and vitreous sampling during vitrectomy. Retrospective case report with slit lamp photography, optical coherence tomography, and fundus photography. A 76-year-old man presented with right eye worsening vision and pain concerning for progressive nodular scleritis and endophthalmitis eight months following a reportedly innocuous tree branch injury. Following the injury, he underwent an MRI, surgical exploration, subconjunctival antibiotic administration, and culturing due to persistent foreign body sensation. Cultures were negative, and the patient was started on oral NSAIDs, oral prednisone, and periocular triamcinolone injections following negative/normal infectious and rheumatologic workup for scleritis. The patient was referred for worsened scleritis with development of endophthalmitis. He underwent lamellar sclerectomy, debridement, and culture of purulent material from scleral nodules in coordination with diagnostic vitrectomy, vitreous sampling, and subconjunctival and intravitreal antibiotic and antifungal treatment. Broad range PCR was positive for Aspergillus fumigatus and targeted antifungal treatment initiated. The eye did not regain visual function and was enucleated for progressive pain six months following diagnosis. Fungal scleritis and endophthalmitis results in significant morbidity. Diagnostic vitrectomy and broad range PCR can aid in prompt diagnosis and targeted treatment, and may be useful in refractory cases.