Endophthalmitis caused by fungi is commonly diagnosed around the world in apparently healthy and immunocompromised individuals. An accurate clinical diagnosis for endophthalmitis confirmed by laboratory techniques is essential for early treatment with antifungal drugs, such as amphotericin B, imidazoles, and other antifungals. Here, we review endophthalmitis caused by fungi according to its classification into endogenous fungal endophthalmitis (EFE) and exogenous fungal endophthalmitis (EXFE). EFE is caused by endogenously acquired fungi, whereas the traumatic implantation of opportunistic fungal pathogens is the main feature of EXFE. We highlight the most important etiologies causing endophthalmitis and the steps required for a rapid diagnosis and management.