A case of endogenous fungous endophthalmitis with secondary pupillary block glaucoma and corneal invasion requiring penetrating keratoplasty is reported. Initially Paecilomyces lilacinus was isolated from a vitreous and a lens aspirate, but a second vitreous tap revealed Aspergillus fumigatus and P lilacinus. This case highlights the difficulty of diagnosing endogenous fungous endophthalmitis presenting without risk factors and the difficulties of managing such cases using the antifungous agents available. To our knowledge, this is the first case report documenting a progression to stromal keratitis from endogenous endophthalmitis secondary to P lilacinus.