We report a case of invasive fungal infection with necrotizing conjunctivitis, scleritis and unilateral panuveitis caused by Scedosporium apiospermum in a 78-year-old woman that developed neutropenia by drugs indicated for rheumatoid arthritis. The etiological diagnosis was confirmed by mycological culture of an ocular secretion with the support of MALDI-TOF-TOF analysis and histopathological findings. The treatment involved surgical debridements together with topical solution and systemic therapy with voriconazole and steroids with a favorable evolution after 2 months of treatment. A relapse required a second therapeutic course for an additional 12 months with improvement and eradication of the agent. Fungal conjunctivitis due to S. apiospermum is a rare event associated with immunosuppressed patients. Its treatment involves surgical debridements and prolonged antifungal therapy.