Purpose With increased use of immunosuppressive and broad-spectrum antimycotic agents as well as increased numbers of immunocompromised individuals and diabetics, non-albicans Candida species infections have significantly increased. Due to the resistance seen in these organisms to commonly used antimycotic agents and intolerance seen with amphotericin B, newer alternative agents need to be explored for use in these infections. Inadequate investigation of the central nervous system and vitreous penetration of caspofungin has been performed. Methods A case of C. glabrata endophthalmitis in a patient with a long-term central intravenous catheter treated successfully with caspofungin is the basis of this study. Results Complete resolution of the infection without relapse occurred after the patient had completed a 28-day course of intravenous caspofungin. The implemented drug regimen, which was adjusted for hepatic impairment, consisted of 50 mg on the first day, followed by 35 mg on subsequent days. Caspofungin was well tolerated without adverse effects. Conclusions C. glabrata is an emerging pathogen often resistant to azole antifungals. This case illustrates that caspofungin penetrates the vitreous and may be an alternative agent for treatment of fungal endophthalmitis secondary to this pathogen in patients intolerant of or infections refractory to other antifungal agents.